--- /dev/null
+package Maasha::Biopieces;
+
+
+# Copyright (C) 2007-2008 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+# Routines for manipulation, parsing and emitting of human/machine readable biotool records.
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use strict;
+use Data::Dumper;
+use Getopt::Long qw( :config bundling );
+use Time::HiRes qw( gettimeofday );
+use Storable qw( dclone );
+use Maasha::Config;
+use Maasha::Common;
+use Maasha::Fasta;
+use Maasha::Align;
+use Maasha::Matrix;
+use Maasha::Match;
+use Maasha::EMBL;
+use Maasha::Stockholm;
+use Maasha::Seq;
+use Maasha::Patscan;
+use Maasha::Plot;
+use Maasha::Calc;
+use Maasha::UCSC;
+use Maasha::NCBI;
+use Maasha::GFF;
+use Maasha::TwoBit;
+use Maasha::Solid;
+use Maasha::SQL;
+
+use vars qw( @ISA @EXPORT_OK );
+
+require Exporter;
+
+@ISA = qw( Exporter );
+
+@EXPORT_OK = qw(
+ read_stream
+ write_stream
+ get_record
+ put_record
+);
+
+use constant {
+ SEQ_NAME => 0,
+ SEQ => 1,
+};
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SIGNAL HANDLER <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+$SIG{ '__DIE__' } = \&sig_handler;
+$SIG{ 'INT' } = \&sig_handler;
+$SIG{ 'TERM' } = \&sig_handler;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GLOBALS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $script, $TMP_DIR );
+
+$script = &Maasha::Common::get_scriptname();
+$TMP_DIR = &Maasha::Common::get_tmpdir();
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LOG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my $log_fh = &Maasha::Common::append_open( $ENV{ "LOG_DIR" } . "/biopieces.log" );
+
+$log_fh->autoflush( 1 );
+
+&log( $log_fh, $script, \@ARGV );
+
+close $log_fh;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RUN SCRIPT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my $t0 = gettimeofday();
+
+&run_script( $script );
+
+my $t1 = gettimeofday();
+
+print STDERR "Program: $script" . ( " " x ( 25 - length( $script ) ) ) . sprintf( "Run time: %.4f\n", ( $t1 - $t0 ) );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub log
+{
+ # Martin A. Hansen, January 2008.
+
+ # Log messages to logfile.
+
+ my ( $fh, # filehandle to logfile
+ $script, # script name
+ $argv, # reference to @ARGV
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $time_stamp, $user );
+
+ $time_stamp = &Maasha::Common::time_stamp();
+
+ $user = $ENV{ "USER" };
+
+ $script = "biopieces" if $script eq "-e";
+
+ print $fh "$time_stamp\t$user\t$script ", join( " ", @{ $argv } ), "\n";
+}
+
+
+sub run_script
+{
+ # Martin A. Hansen, August 2007.
+
+ # Run a specific script.
+
+ my ( $script, # script name
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $options, $in, $out );
+
+ &script_list_biotools( $ENV{ 'INST_DIR'} . "/biotools/usage/" ) if $script eq "list_biotools";
+
+ &script_print_usage( $ENV{ 'INST_DIR'} . "/biotools/usage/$script" ) if -t STDIN and not @ARGV;
+
+ $options = &get_options( $script );
+
+ $in = &read_stream( $options->{ "stream_in" } );
+ $out = &write_stream( $options->{ "stream_out" } );
+
+ if ( $script eq "read_fasta" ) { &script_read_fasta( $in, $out, $options ) }
+ elsif ( $script eq "read_align" ) { &script_read_align( $in, $out, $options ) }
+ elsif ( $script eq "read_tab" ) { &script_read_tab( $in, $out, $options ) }
+ elsif ( $script eq "read_psl" ) { &script_read_psl( $in, $out, $options ) }
+ elsif ( $script eq "read_bed" ) { &script_read_bed( $in, $out, $options ) }
+ elsif ( $script eq "read_blast_tab" ) { &script_read_blast_tab( $in, $out, $options ) }
+ elsif ( $script eq "read_embl" ) { &script_read_embl( $in, $out, $options ) }
+ elsif ( $script eq "read_stockholm" ) { &script_read_stockholm( $in, $out, $options ) }
+ elsif ( $script eq "read_phastcons" ) { &script_read_phastcons( $in, $out, $options ) }
+ elsif ( $script eq "read_soft" ) { &script_read_soft( $in, $out, $options ) }
+ elsif ( $script eq "read_gff" ) { &script_read_gff( $in, $out, $options ) }
+ elsif ( $script eq "read_2bit" ) { &script_read_2bit( $in, $out, $options ) }
+ elsif ( $script eq "read_solexa" ) { &script_read_solexa( $in, $out, $options ) }
+ elsif ( $script eq "read_solid" ) { &script_read_solid( $in, $out, $options ) }
+ elsif ( $script eq "read_mysql" ) { &script_read_mysql( $in, $out, $options ) }
+ elsif ( $script eq "count_seq" ) { &script_count_seq( $in, $out, $options ) }
+ elsif ( $script eq "length_seq" ) { &script_length_seq( $in, $out, $options ) }
+ elsif ( $script eq "uppercase_seq" ) { &script_uppercase_seq( $in, $out, $options ) }
+ elsif ( $script eq "shuffle_seq" ) { &script_shuffle_seq( $in, $out, $options ) }
+ elsif ( $script eq "analyze_seq" ) { &script_analyze_seq( $in, $out, $options ) }
+ elsif ( $script eq "analyze_tags" ) { &script_analyze_tags( $in, $out, $options ) }
+ elsif ( $script eq "complexity_seq" ) { &script_complexity_seq( $in, $out, $options ) }
+ elsif ( $script eq "oligo_freq" ) { &script_oligo_freq( $in, $out, $options ) }
+ elsif ( $script eq "create_weight_matrix" ) { &script_create_weight_matrix( $in, $out, $options ) }
+ elsif ( $script eq "calc_bit_scores" ) { &script_calc_bit_scores( $in, $out, $options ) }
+ elsif ( $script eq "reverse_seq" ) { &script_reverse_seq( $in, $out, $options ) }
+ elsif ( $script eq "complement_seq" ) { &script_complement_seq( $in, $out, $options ) }
+ elsif ( $script eq "remove_indels" ) { &script_remove_indels( $in, $out, $options ) }
+ elsif ( $script eq "transliterate_seq" ) { &script_transliterate_seq( $in, $out, $options ) }
+ elsif ( $script eq "transliterate_vals" ) { &script_transliterate_vals( $in, $out, $options ) }
+ elsif ( $script eq "translate_seq" ) { &script_translate_seq( $in, $out, $options ) }
+ elsif ( $script eq "extract_seq" ) { &script_extract_seq( $in, $out, $options ) }
+ elsif ( $script eq "get_genome_seq" ) { &script_get_genome_seq( $in, $out, $options ) }
+ elsif ( $script eq "get_genome_align" ) { &script_get_genome_align( $in, $out, $options ) }
+ elsif ( $script eq "get_genome_phastcons" ) { &script_get_genome_phastcons( $in, $out, $options ) }
+ elsif ( $script eq "fold_seq" ) { &script_fold_seq( $in, $out, $options ) }
+ elsif ( $script eq "split_seq" ) { &script_split_seq( $in, $out, $options ) }
+ elsif ( $script eq "split_bed" ) { &script_split_bed( $in, $out, $options ) }
+ elsif ( $script eq "align_seq" ) { &script_align_seq( $in, $out, $options ) }
+ elsif ( $script eq "tile_seq" ) { &script_tile_seq( $in, $out, $options ) }
+ elsif ( $script eq "invert_align" ) { &script_invert_align( $in, $out, $options ) }
+ elsif ( $script eq "patscan_seq" ) { &script_patscan_seq( $in, $out, $options ) }
+ elsif ( $script eq "create_blast_db" ) { &script_create_blast_db( $in, $out, $options ) }
+ elsif ( $script eq "blast_seq" ) { &script_blast_seq( $in, $out, $options ) }
+ elsif ( $script eq "blat_seq" ) { &script_blat_seq( $in, $out, $options ) }
+ elsif ( $script eq "match_seq" ) { &script_match_seq( $in, $out, $options ) }
+ elsif ( $script eq "create_vmatch_index" ) { &script_create_vmatch_index( $in, $out, $options ) }
+ elsif ( $script eq "vmatch_seq" ) { &script_vmatch_seq( $in, $out, $options ) }
+ elsif ( $script eq "write_fasta" ) { &script_write_fasta( $in, $out, $options, $options ) }
+ elsif ( $script eq "write_align" ) { &script_write_align( $in, $out, $options ) }
+ elsif ( $script eq "write_blast" ) { &script_write_blast( $in, $out, $options ) }
+ elsif ( $script eq "write_tab" ) { &script_write_tab( $in, $out, $options ) }
+ elsif ( $script eq "write_bed" ) { &script_write_bed( $in, $out, $options ) }
+ elsif ( $script eq "write_psl" ) { &script_write_psl( $in, $out, $options ) }
+ elsif ( $script eq "write_2bit" ) { &script_write_2bit( $in, $out, $options, $options ) }
+ elsif ( $script eq "write_solid" ) { &script_write_solid( $in, $out, $options, $options ) }
+ elsif ( $script eq "head_records" ) { &script_head_records( $in, $out, $options ) }
+ elsif ( $script eq "remove_keys" ) { &script_remove_keys( $in, $out, $options ) }
+ elsif ( $script eq "rename_keys" ) { &script_rename_keys( $in, $out, $options ) }
+ elsif ( $script eq "uniq_vals" ) { &script_uniq_vals( $in, $out, $options ) }
+ elsif ( $script eq "merge_vals" ) { &script_merge_vals( $in, $out, $options ) }
+ elsif ( $script eq "grab" ) { &script_grab( $in, $out, $options ) }
+ elsif ( $script eq "compute" ) { &script_compute( $in, $out, $options ) }
+ elsif ( $script eq "flip_tab" ) { &script_flip_tab( $in, $out, $options ) }
+ elsif ( $script eq "add_ident" ) { &script_add_ident( $in, $out, $options ) }
+ elsif ( $script eq "count_records" ) { &script_count_records( $in, $out, $options ) }
+ elsif ( $script eq "random_records" ) { &script_random_records( $in, $out, $options ) }
+ elsif ( $script eq "sort_records" ) { &script_sort_records( $in, $out, $options ) }
+ elsif ( $script eq "count_vals" ) { &script_count_vals( $in, $out, $options ) }
+ elsif ( $script eq "plot_histogram" ) { &script_plot_histogram( $in, $out, $options ) }
+ elsif ( $script eq "plot_lendist" ) { &script_plot_lendist( $in, $out, $options ) }
+ elsif ( $script eq "plot_chrdist" ) { &script_plot_chrdist( $in, $out, $options ) }
+ elsif ( $script eq "plot_karyogram" ) { &script_plot_karyogram( $in, $out, $options ) }
+ elsif ( $script eq "plot_matches" ) { &script_plot_matches( $in, $out, $options ) }
+ elsif ( $script eq "plot_seqlogo" ) { &script_plot_seqlogo( $in, $out, $options ) }
+ elsif ( $script eq "plot_phastcons_profiles" ) { &script_plot_phastcons_profiles( $in, $out, $options ) }
+ elsif ( $script eq "analyze_bed" ) { &script_analyze_bed( $in, $out, $options ) }
+ elsif ( $script eq "analyze_vals" ) { &script_analyze_vals( $in, $out, $options ) }
+ elsif ( $script eq "length_vals" ) { &script_length_vals( $in, $out, $options ) }
+ elsif ( $script eq "sum_vals" ) { &script_sum_vals( $in, $out, $options ) }
+ elsif ( $script eq "mean_vals" ) { &script_mean_vals( $in, $out, $options ) }
+ elsif ( $script eq "median_vals" ) { &script_median_vals( $in, $out, $options ) }
+ elsif ( $script eq "max_vals" ) { &script_max_vals( $in, $out, $options ) }
+ elsif ( $script eq "min_vals" ) { &script_min_vals( $in, $out, $options ) }
+ elsif ( $script eq "upload_to_ucsc" ) { &script_upload_to_ucsc( $in, $out, $options ) }
+
+ close $in if defined $in;
+ close $out;
+
+ # unset status - missing
+ # write log file - missing
+}
+
+
+sub get_options
+{
+ # Martin A. Hansen, February 2008.
+
+ # Gets options from commandline and checks these vigerously.
+
+ my ( $script, # name of script
+ ) = @_;
+
+ # Returns hash
+
+ my ( %options, @options, $opt, @genomes );
+
+ if ( $script eq "read_fasta" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ );
+ }
+ elsif ( $script eq "read_align" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ );
+ }
+ elsif ( $script eq "read_tab" )
+ {
+ @options = qw(
+ data_in|i=s
+ delimit|d=s
+ cols|c=s
+ keys|k=s
+ skip|s=s
+ num|n=s
+ );
+ }
+ elsif ( $script eq "read_psl" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ );
+ }
+ elsif ( $script eq "read_bed" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ );
+ }
+ elsif ( $script eq "read_blast_tab" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ );
+ }
+ elsif ( $script eq "read_embl" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ keys|k=s
+ feats|f=s
+ quals|q=s
+ );
+ }
+ elsif ( $script eq "read_stockholm" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ );
+ }
+ elsif ( $script eq "read_phastcons" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ min|m=s
+ dist|d=s
+ threshold|t=f
+ gap|g=s
+ );
+ }
+ elsif ( $script eq "read_soft" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ );
+ }
+ elsif ( $script eq "read_gff" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ );
+ }
+ elsif ( $script eq "read_2bit" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ no_mask|N
+ );
+ }
+ elsif ( $script eq "read_solexa" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ quality|q=s
+ );
+ }
+ elsif ( $script eq "read_solid" )
+ {
+ @options = qw(
+ data_in|i=s
+ num|n=s
+ quality|q=s
+ );
+ }
+ elsif ( $script eq "read_mysql" )
+ {
+ @options = qw(
+ database|d=s
+ query|q=s
+ user|u=s
+ password|p=s
+ );
+ }
+ elsif ( $script eq "count_seq" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ );
+ }
+ elsif ( $script eq "length_seq" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ );
+ }
+ elsif ( $script eq "oligo_freq" )
+ {
+ @options = qw(
+ word_size|w=s
+ all|a
+ );
+ }
+ elsif ( $script eq "create_weight_matrix" )
+ {
+ @options = qw(
+ percent|p
+ );
+ }
+ elsif ( $script eq "transliterate_seq" )
+ {
+ @options = qw(
+ search|s=s
+ replace|r=s
+ delete|d=s
+ );
+ }
+ elsif ( $script eq "transliterate_vals" )
+ {
+ @options = qw(
+ keys|k=s
+ search|s=s
+ replace|r=s
+ delete|d=s
+ );
+ }
+ elsif ( $script eq "translate_seq" )
+ {
+ @options = qw(
+ frames|f=s
+ );
+ }
+ elsif ( $script eq "extract_seq" )
+ {
+ @options = qw(
+ beg|b=s
+ end|e=s
+ len|l=s
+ );
+ }
+ elsif ( $script eq "get_genome_seq" )
+ {
+ @options = qw(
+ genome|g=s
+ chr|c=s
+ beg|b=s
+ end|e=s
+ len|l=s
+ flank|f=s
+ mask|m
+ );
+ }
+ elsif ( $script eq "get_genome_align" )
+ {
+ @options = qw(
+ genome|g=s
+ chr|c=s
+ beg|b=s
+ end|e=s
+ len|l=s
+ strand|s=s
+ );
+ }
+ elsif ( $script eq "get_genome_phastcons" )
+ {
+ @options = qw(
+ genome|g=s
+ chr|c=s
+ beg|b=s
+ end|e=s
+ len|l=s
+ flank|f=s
+ );
+ }
+ elsif ( $script eq "split_seq" )
+ {
+ @options = qw(
+ word_size|w=s
+ uniq|u
+ );
+ }
+ elsif ( $script eq "split_bed" )
+ {
+ @options = qw(
+ window_size|w=s
+ step_size|s=s
+ );
+ }
+ elsif ( $script eq "tile_seq" )
+ {
+ @options = qw(
+ identity|i=s
+ supress_indels|s
+ );
+ }
+ elsif ( $script eq "invert_align" )
+ {
+ @options = qw(
+ soft|s
+ );
+ }
+ elsif ( $script eq "patscan_seq" )
+ {
+ @options = qw(
+ patterns|p=s
+ patterns_in|P=s
+ comp|c
+ max_hits|h=s
+ max_misses|m=s
+ genome|g=s
+ );
+ }
+ elsif ( $script eq "create_blast_db" )
+ {
+ @options = qw(
+ no_stream|x
+ database|d=s
+ );
+ }
+ elsif ( $script eq "blast_seq" )
+ {
+ @options = qw(
+ database|d=s
+ genome|g=s
+ program|p=s
+ e_val|e=f
+ filter|f
+ cpus|c=s
+ no_filter|F
+ );
+ }
+ elsif ( $script eq "blat_seq" )
+ {
+ @options = qw(
+ genome|g=s
+ tile_size|t=s
+ step_size|s=s
+ min_identity|m=s
+ min_score|M=s
+ one_off|o=s
+ ooc|c
+ );
+ }
+ elsif ( $script eq "match_seq" )
+ {
+ @options = qw(
+ word_size|w=s
+ direction|d=s
+ );
+ }
+ elsif ( $script eq "create_vmatch_index" )
+ {
+ @options = qw(
+ index_name|i=s
+ prefix_length|p=s
+ no_stream|x
+ );
+ }
+ elsif ( $script eq "vmatch_seq" )
+ {
+ @options = qw(
+ genome|g=s
+ index_name|i=s
+ count|c
+ max_hits|m=s
+ hamming_dist|h=s
+ edit_dist|e=s
+ );
+ }
+ elsif ( $script eq "write_fasta" )
+ {
+ @options = qw(
+ wrap|w=s
+ no_stream|x
+ data_out|o=s
+ compress|Z
+ );
+ }
+ elsif ( $script eq "write_align" )
+ {
+ @options = qw(
+ wrap|w=s
+ no_stream|x
+ no_ruler|R
+ no_consensus|C
+ data_out|o=s
+ );
+ }
+ elsif ( $script eq "write_blast" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ comment|c
+ compress|Z
+ );
+ }
+ elsif ( $script eq "write_tab" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ delimit|d=s
+ keys|k=s
+ no_keys|K=s
+ comment|c
+ compress|Z
+ );
+ }
+ elsif ( $script eq "write_bed" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ compress|Z
+ );
+ }
+ elsif ( $script eq "write_psl" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ compress|Z
+ );
+ }
+ elsif ( $script eq "write_2bit" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ no_mask|N
+ );
+ }
+ elsif ( $script eq "write_solid" )
+ {
+ @options = qw(
+ wrap|w=s
+ no_stream|x
+ data_out|o=s
+ compress|Z
+ );
+ }
+ elsif ( $script eq "plot_seqlogo" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ );
+ }
+ elsif ( $script eq "plot_phastcons_profiles" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ genome|g=s
+ mean|m
+ median|M
+ flank|f=s
+ terminal|t=s
+ title|T=s
+ xlabel|X=s
+ ylabel|Y=s
+ );
+ }
+ elsif ( $script eq "analyze_vals" )
+ {
+ @options = qw(
+ no_stream|x
+ keys|k=s
+ );
+ }
+ elsif ( $script eq "head_records" )
+ {
+ @options = qw(
+ num|n=s
+ );
+ }
+ elsif ( $script eq "remove_keys" )
+ {
+ @options = qw(
+ keys|k=s
+ save_keys|K=s
+ );
+ }
+ elsif ( $script eq "rename_keys" )
+ {
+ @options = qw(
+ keys|k=s
+ );
+ }
+ elsif ( $script eq "uniq_vals" )
+ {
+ @options = qw(
+ key|k=s
+ invert|i
+ );
+ }
+ elsif ( $script eq "merge_vals" )
+ {
+ @options = qw(
+ keys|k=s
+ delimit|d=s
+ );
+ }
+ elsif ( $script eq "grab" )
+ {
+ @options = qw(
+ patterns|p=s
+ patterns_in|P=s
+ regex|r=s
+ eval|e=s
+ exact_in|E=s
+ invert|i
+ case_insensitive|c
+ keys|k=s
+ keys_only|K
+ vals_only|V
+ );
+ }
+ elsif ( $script eq "compute" )
+ {
+ @options = qw(
+ eval|e=s
+ );
+ }
+ elsif ( $script eq "add_ident" )
+ {
+ @options = qw(
+ prefix|p=s
+ key|k=s
+ );
+ }
+ elsif ( $script eq "count_records" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ );
+ }
+ elsif ( $script eq "random_records" )
+ {
+ @options = qw(
+ num|n=s
+ );
+ }
+ elsif ( $script eq "sort_records" )
+ {
+ @options = qw(
+ reverse|r
+ keys|k=s
+ );
+ }
+ elsif ( $script eq "count_vals" )
+ {
+ @options = qw(
+ keys|k=s
+ );
+ }
+ elsif ( $script eq "plot_histogram" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ terminal|t=s
+ title|T=s
+ xlabel|X=s
+ ylabel|Y=s
+ key|k=s
+ sort|s=s
+ );
+ }
+ elsif ( $script eq "plot_lendist" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ terminal|t=s
+ title|T=s
+ xlabel|X=s
+ ylabel|Y=s
+ key|k=s
+ );
+ }
+ elsif ( $script eq "plot_chrdist" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ terminal|t=s
+ title|T=s
+ xlabel|X=s
+ ylabel|Y=s
+ );
+ }
+ elsif ( $script eq "plot_karyogram" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ genome|g=s
+ feat_color|f=s
+ );
+ }
+ elsif ( $script eq "plot_matches" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ terminal|t=s
+ title|T=s
+ xlabel|X=s
+ ylabel|Y=s
+ direction|d=s
+ );
+ }
+ elsif ( $script eq "length_vals" )
+ {
+ @options = qw(
+ keys|k=s
+ );
+ }
+ elsif ( $script eq "sum_vals" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ keys|k=s
+ );
+ }
+ elsif ( $script eq "mean_vals" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ keys|k=s
+ );
+ }
+ elsif ( $script eq "median_vals" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ keys|k=s
+ );
+ }
+ elsif ( $script eq "max_vals" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ keys|k=s
+ );
+ }
+ elsif ( $script eq "min_vals" )
+ {
+ @options = qw(
+ no_stream|x
+ data_out|o=s
+ keys|k=s
+ );
+ }
+ elsif ( $script eq "upload_to_ucsc" )
+ {
+ @options = qw(
+ no_stream|x
+ database|d=s
+ table|t=s
+ short_label|s=s
+ long_label|l=s
+ group|g=s
+ priority|p=f
+ use_score|u
+ visibility|v=s
+ wiggle|w
+ color|c=s
+ chunk_size|C=s
+ );
+ }
+
+ push @options, qw(
+ stream_in|I=s
+ stream_out|O=s
+ verbose
+ );
+
+# print STDERR Dumper( \@options );
+
+ GetOptions(
+ \%options,
+ @options,
+ );
+
+ $options{ "cols" } = [ split ",", $options{ "cols" } ] if defined $options{ "cols" };
+ $options{ "keys" } = [ split ",", $options{ "keys" } ] if defined $options{ "keys" };
+ $options{ "no_keys" } = [ split ",", $options{ "no_keys" } ] if defined $options{ "no_keys" };
+ $options{ "save_keys" } = [ split ",", $options{ "save_keys" } ] if defined $options{ "save_keys" };
+ $options{ "quals" } = [ split ",", $options{ "quals" } ] if defined $options{ "quals" };
+ $options{ "feats" } = [ split ",", $options{ "feats" } ] if defined $options{ "feats" };
+ $options{ "frames" } = [ split ",", $options{ "frames" } ] if defined $options{ "frames" };
+
+ # ---- check arguments ----
+
+ if ( $options{ 'data_in' } )
+ {
+ $options{ "files" } = &getopt_files( $options{ 'data_in' } );
+
+ &Maasha::Common::error( qq(Argument to --data_in must be a valid file or fileglob expression) ) if scalar @{ $options{ "files" } } == 0;
+ }
+
+ map { &Maasha::Common::error( qq(Argument to --cols must be a whole numbers - not "$_") ) if $_ !~ /^\d+$/ } @{ $options{ "cols" } } if $options{ "cols" };
+
+# print STDERR Dumper( \%options );
+
+ foreach $opt ( keys %options )
+ {
+ if ( $opt =~ /stream_in|pattern_in|exact_in/ and not -f $options{ $opt } )
+ {
+ &Maasha::Common::error( qq(Argument to --$opt must be a valid file or fileglob expression - not "$options{ $opt }") );
+ }
+ elsif ( $opt =~ /beg|end|word_size|wrap|chunk_size|tile_size|len|prefix_length|num|skip|cpus|window_size|step_size/ and $options{ $opt } !~ /^\d+$/ )
+ {
+ &Maasha::Common::error( qq(Argument to --$opt must be a whole number - not "$options{ $opt }") );
+ }
+ elsif ( $opt =~ /max_hits|max_hits|max_misses|dist|edit_dist|flank|gap|hamming_dist|priority/ and $options{ $opt } !~ /^-?\d+$/ )
+ {
+ &Maasha::Common::error( qq(Argument to --$opt must be an integer - not "$options{ $opt }") );
+ }
+ elsif ( $opt =~ /identity|threshold/ and $options{ $opt } !~ /^-?(?:\d+(?:\.\d*)?|\.\d+)$/ )
+ {
+ &Maasha::Common::error( qq(Argument to --$opt must be a decimal number - not "$options{ $opt }") );
+ }
+ elsif ( $opt =~ /e_val/ and $options{ $opt } !~ /^([+-]?)(?=\d|\.\d)\d*(\.\d*)?([Ee]([+-]?\d+))?$/ )
+ {
+ &Maasha::Common::error( qq(Argument to --$opt must be a float - not "$options{ $opt }") );
+ }
+ elsif ( $opt =~ /strand/ and $options{ $opt } !~ /^(\+|-)$/ )
+ {
+ &Maasha::Common::error( qq(Argument to --$opt must be "+" or "-" - not "$options{ $opt }") );
+ }
+ elsif ( $opt eq "genome" )
+ {
+ @genomes = &Maasha::Config::genomes();
+
+ if ( not grep $options{ $opt }, @genomes ) {
+ &Maasha::Common::error( qq(Genome $options{ $opt } not found in "$ENV{ 'INST_DIR' }/conf/genomes.conf") );
+ }
+ }
+ elsif ( $opt eq "terminal" and not $options{ $opt } =~ /^(svg|post|dumb)/ )
+ {
+ &Maasha::Common::error( qq(Bad --$opt argument "$options{ $opt }") );
+ }
+ elsif ( $opt eq "table" and $options{ $opt } =~ /-\./ )
+ {
+ &Maasha::Common::error( qq(Character '$options{ $opt }' is not allowed in table names) );
+ }
+ }
+
+ &Maasha::Common::error( qq(no --database specified) ) if $script eq "create_blast_db" and not $options{ "database" };
+ &Maasha::Common::error( qq(no --index_name specified) ) if $script eq "create_vmatch_index" and not $options{ "index_name" };
+ &Maasha::Common::error( qq(no --database or --genome specified) ) if $script eq "blast_seq" and not $options{ "genome" } and not $options{ "database" };
+ &Maasha::Common::error( qq(both --database and --genome specified) ) if $script eq "blast_seq" and $options{ "genome" } and $options{ "database" };
+ &Maasha::Common::error( qq(no --index_name or --genome specified) ) if $script eq "vmatch_seq" and not $options{ "genome" } and not $options{ "index_name" };
+ &Maasha::Common::error( qq(both --index and --genome specified) ) if $script eq "vmatch_seq" and $options{ "genome" } and $options{ "index" };
+ &Maasha::Common::error( qq(no --genome specified) ) if $script =~ /get_genome_seq|get_genome_align|get_genome_phastcons|blat_seq|plot_phastcons_profiles|plot_karyogram/ and not $options{ "genome" };
+ &Maasha::Common::error( qq(no --key specified) ) if $script =~ /plot_lendist|plot_histogram/ and not $options{ "key" };
+ &Maasha::Common::error( qq(no --keys speficied) ) if $script =~ /sort_records|count_vals|sum_vals|mean_vals|median_vals|length_vals/ and not $options{ "keys" };
+
+ if ( $script eq "upload_to_ucsc" )
+ {
+ &Maasha::Common::error( qq(no --database specified) ) if not $options{ "database" };
+ &Maasha::Common::error( qq(no --table specified) ) if not $options{ "table" };
+ }
+
+ return wantarray ? %options : \%options;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SCRIPTS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub script_print_usage
+{
+ # Martin A. Hansen, January 2008.
+
+ # Retrieves usage information from file and
+ # prints this nicely formatted.
+
+ my ( $path, # full path to usage file
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $script, $fh, $line, @lines, @list, %hash, $key );
+
+ $script = ( split "/", $path )[ -1 ];
+
+ $fh = &Maasha::Common::read_open( $path );
+
+ push @list, "Program name";
+
+ $hash{ "Program name" } = [ $script ];
+
+ while ( $line = <$fh> )
+ {
+ chomp $line;
+
+ $line =~ s/\$script/$script/g;
+
+ if ( $line =~ /^([^:]+):\s+(.+)$/ )
+ {
+ push @list, $1 if not exists $hash{ $1 };
+ push @{ $hash{ $1 } }, $2;
+ }
+ }
+
+ close $fh;
+
+ print "\n";
+
+ foreach $key ( @list )
+ {
+ if ( scalar @{ $hash{ $key } } == 1 )
+ {
+ @lines = &Maasha::Common::wrap_line( $hash{ $key }->[ 0 ], 80 );
+
+ printf( "%-15s%s\n", "$key:", shift @lines );
+
+ map { printf( "%-15s%s\n", "", $_ ) } @lines;
+
+ print "\n";
+ }
+ else
+ {
+ print "$key:\n";
+
+ map { print " $_\n" } @{ $hash{ $key } };
+
+ print "\n";
+ }
+ }
+
+ exit;
+}
+
+
+sub script_list_biotools
+{
+ # Martin A. Hansen, January 2008.
+
+ # Prints the description from the usage for each of the biotools.
+
+ my ( $path, # full path to usage directory
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( @files, $file, $fh, $line, @lines, $program );
+
+ @files = &Maasha::Common::ls_files( $path );
+
+ foreach $file ( sort @files )
+ {
+ $program = ( split "/", $file )[ -1 ];
+
+ $fh = &Maasha::Common::read_open( $file );
+
+ while ( $line = <$fh> )
+ {
+ chomp $line;
+
+ if ( $line =~ /^Description:\s+(.+)/ )
+ {
+ @lines = &Maasha::Common::wrap_line( $1, 60 );
+
+ printf( "%-30s%s\n", $program, shift @lines );
+
+ map { printf( "%-30s%s\n", "", $_ ) } @lines;
+ }
+ }
+
+ close $fh;
+ }
+
+ exit;
+}
+
+
+sub script_read_fasta
+{
+ # Martin A. Hansen, August 2007.
+
+ # Read sequences from FASTA file.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $file, $data_in, $entry, $num );
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+
+ while ( $entry = &Maasha::Fasta::get_entry( $data_in ) )
+ {
+ if ( defined $entry->[ SEQ_NAME ] and $entry->[ SEQ ] )
+ {
+ $record = {
+ SEQ_NAME => $entry->[ SEQ_NAME ],
+ SEQ => $entry->[ SEQ ],
+ SEQ_LEN => length $entry->[ SEQ ],
+ };
+
+ &put_record( $record, $out );
+ }
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_align
+{
+ # Martin A. Hansen, August 2007.
+
+ # Read aligned sequences from FASTA file.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $entry, $record, $file, $data_in, $num );
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+
+ while ( $entry = &Maasha::Fasta::get_entry( $data_in ) )
+ {
+ if ( $entry->[ SEQ_NAME ] and $entry->[ SEQ ] )
+ {
+ $record = {
+ ALIGN => 1,
+ SEQ_NAME => $entry->[ SEQ_NAME ],
+ SEQ => $entry->[ SEQ ],
+ ALIGN_LEN => length $entry->[ SEQ ],
+ };
+
+ &put_record( $record, $out );
+ }
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_tab
+{
+ # Martin A. Hansen, August 2007.
+
+ # Read table or table columns from stream or file.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $file, $line, @fields, @fields2, $i, $record, $data_in, $skip, $num );
+
+ $options->{ 'delimit' } ||= '\s+';
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $skip = $options->{ 'skip' } ||= 0;
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+
+ while ( $line = <$data_in> )
+ {
+ if ( $skip )
+ {
+ $skip--;
+ next;
+ }
+
+ next if $line =~ /^#|^$/;
+
+ chomp $line;
+
+ undef $record;
+ undef @fields2;
+
+ @fields = split /$options->{'delimit'}/, $line;
+
+ if ( $options->{ "cols" } ) {
+ map { push @fields2, $fields[ $_ ] } @{ $options->{ "cols" } };
+ } else {
+ @fields2 = @fields;
+ }
+
+ for ( $i = 0; $i < @fields2; $i++ )
+ {
+ if ( $options->{ "keys" }->[ $i ] ) {
+ $record->{ $options->{ "keys" }->[ $i ] } = $fields2[ $i ];
+ } else {
+ $record->{ "V" . $i } = $fields2[ $i ];
+ }
+ }
+
+ &put_record( $record, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_psl
+{
+ # Martin A. Hansen, August 2007.
+
+ # Read psl table from stream or file.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, @files, $file, $entries, $entry, $num );
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $entries = &Maasha::UCSC::psl_get_entries( $file );
+
+ foreach $entry ( @{ $entries } )
+ {
+ &put_record( $entry, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+ }
+
+ NUM:
+}
+
+
+sub script_read_bed
+{
+ # Martin A. Hansen, August 2007.
+
+ # Read bed table from stream or file.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $file, $record, $entry, $data_in, $num );
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+
+ while ( $entry = &Maasha::UCSC::bed_get_entry( $data_in ) )
+ {
+ &put_record( $entry, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_blast_tab
+{
+ # Martin A. Hansen, September 2007.
+
+ # Read tabular BLAST output from NCBI blast run with -m8 or -m9.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $file, $line, @fields, $strand, $record, $data_in, $num );
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+
+ while ( $line = <$data_in> )
+ {
+ chomp $line;
+
+ next if $line =~ /^#/;
+
+ @fields = split /\t/, $line;
+
+ $record->{ "REC_TYPE" } = "BLAST";
+ $record->{ "Q_ID" } = $fields[ 0 ];
+ $record->{ "S_ID" } = $fields[ 1 ];
+ $record->{ "IDENT" } = $fields[ 2 ];
+ $record->{ "ALIGN_LEN" } = $fields[ 3 ];
+ $record->{ "MISMATCHES" } = $fields[ 4 ];
+ $record->{ "GAPS" } = $fields[ 5 ];
+ $record->{ "Q_BEG" } = $fields[ 6 ] - 1; # BLAST is 1-based
+ $record->{ "Q_END" } = $fields[ 7 ] - 1; # BLAST is 1-based
+ $record->{ "S_BEG" } = $fields[ 8 ] - 1; # BLAST is 1-based
+ $record->{ "S_END" } = $fields[ 9 ] - 1; # BLAST is 1-based
+ $record->{ "E_VAL" } = $fields[ 10 ];
+ $record->{ "BIT_SCORE" } = $fields[ 11 ];
+
+ if ( $record->{ "S_BEG" } > $record->{ "S_END" } )
+ {
+ $record->{ "STRAND" } = '-';
+
+ ( $record->{ "S_BEG" }, $record->{ "S_END" } ) = ( $record->{ "S_END" }, $record->{ "S_BEG" } );
+ }
+ else
+ {
+ $record->{ "STRAND" } = '+';
+ }
+
+ &put_record( $record, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_embl
+{
+ # Martin A. Hansen, August 2007.
+
+ # Read EMBL format.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( %options2, $file, $data_in, $num, $entry, $record );
+
+ map { $options2{ "keys" }{ $_ } = 1 } @{ $options->{ "keys" } };
+ map { $options2{ "feats" }{ $_ } = 1 } @{ $options->{ "feats" } };
+ map { $options2{ "quals" }{ $_ } = 1 } @{ $options->{ "quals" } };
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+
+ while ( $entry = &Maasha::EMBL::get_embl_entry( $data_in ) )
+ {
+ $record = &Maasha::EMBL::parse_embl_entry( $entry, \%options2 );
+
+ my ( $feat, $feat2, $qual, $qual_val, $record_copy );
+
+ $record_copy = dclone $record;
+
+ delete $record_copy->{ "FT" };
+
+ &put_record( $record_copy, $out );
+
+ delete $record_copy->{ "SEQ" };
+
+ foreach $feat ( keys %{ $record->{ "FT" } } )
+ {
+ $record_copy->{ "FEAT_TYPE" } = $feat;
+
+ foreach $feat2 ( @{ $record->{ "FT" }->{ $feat } } )
+ {
+ foreach $qual ( keys %{ $feat2 } )
+ {
+ $qual_val = join "; ", @{ $feat2->{ $qual } };
+
+ $qual =~ s/^_//;
+ $qual = uc $qual;
+
+ $record_copy->{ $qual } = $qual_val;
+ }
+
+ &put_record( $record_copy, $out );
+ }
+ }
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_stockholm
+{
+ # Martin A. Hansen, August 2007.
+
+ # Read Stockholm format.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $data_in, $file, $num, $entry, $record, $record_anno, $record_align, $key, $seq );
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+
+ while ( $entry = &Maasha::Stockholm::get_stockholm_entry( $data_in ) )
+ {
+ $record = &Maasha::Stockholm::parse_stockholm_entry( $entry );
+
+ undef $record_anno;
+
+ foreach $key ( keys %{ $record->{ "GF" } } ) {
+ $record_anno->{ $key } = $record->{ "GF" }->{ $key };
+ }
+
+ $record_anno->{ "ALIGN" } = $num;
+
+ &put_record( $record_anno, $out );
+
+ foreach $seq ( @{ $record->{ "ALIGN" } } )
+ {
+ undef $record_align;
+
+ $record_align = {
+ ALIGN => $num,
+ SEQ_NAME => $seq->[ 0 ],
+ SEQ => $seq->[ 1 ],
+ };
+
+ &put_record( $record_align, $out );
+ }
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_phastcons
+{
+ # Martin A. Hansen, December 2007.
+
+ # Read PhastCons format.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $data_in, $file, $num, $entry, @records, $record );
+
+ $options->{ "min" } ||= 10;
+ $options->{ "dist" } ||= 25;
+ $options->{ "threshold" } ||= 0.8;
+ $options->{ "gap" } ||= 5;
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+
+ while ( $entry = &Maasha::UCSC::phastcons_get_entry( $data_in ) )
+ {
+ @records = &Maasha::UCSC::phastcons_parse_entry( $entry, $options );
+
+ foreach $record ( @records )
+ {
+ $record->{ "REC_TYPE" } = "BED";
+ $record->{ "BED_LEN" } = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
+
+ &put_record( $record, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_soft
+{
+ # Martin A. Hansen, December 2007.
+
+ # Read soft format.
+ # http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $data_in, $file, $num, $records, $record, $soft_index, $fh, @platforms, $plat_table, @samples, $sample, $old_end );
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $soft_index = &Maasha::NCBI::soft_index_file( $file );
+
+ $fh = &Maasha::Common::read_open( $file );
+
+ @platforms = grep { $_->[ 0 ] =~ /PLATFORM/ } @{ $soft_index };
+
+ $plat_table = &Maasha::NCBI::soft_get_platform( $fh, $platforms[ 0 ]->[ 1 ], $platforms[ -1 ]->[ 2 ] );
+
+ @samples = grep { $_->[ 0 ] =~ /SAMPLE/ } @{ $soft_index };
+
+ $old_end = $platforms[ -1 ]->[ 2 ];
+
+ foreach $sample ( @samples )
+ {
+ $records = &Maasha::NCBI::soft_get_sample( $fh, $plat_table, $sample->[ 1 ] - $old_end - 1, $sample->[ 2 ] - $old_end - 1 );
+
+ foreach $record ( @{ $records } )
+ {
+ &put_record( $record, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ $old_end = $sample->[ 2 ];
+ }
+
+ close $fh;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+ close $fh if $fh;
+}
+
+
+sub script_read_gff
+{
+ # Martin A. Hansen, February 2008.
+
+ # Read soft format.
+ # http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $data_in, $file, $fh, $num, $record, $entry );
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $fh = &Maasha::Common::read_open( $file );
+
+ while ( $entry = &Maasha::GFF::get_entry( $fh ) )
+ {
+ &put_record( $entry, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $fh;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_2bit
+{
+ # Martin A. Hansen, March 2008.
+
+ # Read sequences from 2bit file.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $file, $data_in, $mask, $toc, $line, $num );
+
+ $mask = 1 if not $options->{ "no_mask" };
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+
+ $toc = &Maasha::TwoBit::twobit_get_TOC( $data_in );
+
+ foreach $line ( @{ $toc } )
+ {
+ $record->{ "SEQ_NAME" } = $line->[ 0 ];
+ $record->{ "SEQ" } = &Maasha::TwoBit::twobit_get_seq( $data_in, $line->[ 1 ], undef, undef, $mask );
+ $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
+
+ &put_record( $record, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_solexa
+{
+ # Martin A. Hansen, March 2008.
+
+ # Read Solexa sequence reads from file.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $file, $base_name, $data_in, $line, $num, @fields, @seqs, @scores, $i, $seq, $seq_count );
+
+ $options->{ "quality" } ||= 20;
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+ $base_name = &Maasha::Common::get_basename( $file );
+ $base_name =~ s/\..*//;
+
+ $seq_count = 0;
+
+ while ( $line = <$data_in> )
+ {
+ @fields = split /:/, $line;
+ @seqs = split //, $fields[ 5 ];
+ @scores = split / /, $fields[ -1 ];
+
+ for ( $i = 0; $i < @scores; $i++ ) {
+ $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $options->{ "quality" };
+ }
+
+ $seq = join "", @seqs;
+
+ $record->{ "SEQ_NAME" } = sprintf( "%s_ID%08d", $base_name, $seq_count );
+ $record->{ "SEQ" } = $seq;
+ $record->{ "SEQ_LEN" } = length $seq;
+ $record->{ "SCORE_MEAN" } = sprintf ( "%.2f", &Maasha::Calc::mean( \@scores ) );
+
+ &put_record( $record, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $seq_count++;
+ $num++;
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_solid
+{
+ # Martin A. Hansen, April 2008.
+
+ # Read Solid sequence from file.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $file, $data_in, $line, $num, $seq_name, $seq_cs, $seq_qual, @scores, @seqs, $i );
+
+ $options->{ "quality" } ||= 15;
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $data_in = &Maasha::Common::read_open( $file );
+
+ while ( $line = <$data_in> )
+ {
+ chomp $line;
+
+ ( $seq_name, $seq_cs, $seq_qual ) = split /\t/, $line;
+
+ @scores = split /,/, $seq_qual;
+ @seqs = split //, &Maasha::Solid::color_space2seq( $seq_cs );
+
+ for ( $i = 0; $i < @seqs; $i++ ) {
+ $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $options->{ "quality" };
+ }
+
+ $record = {
+ SEQ_NAME => $seq_name,
+ SEQ_CS => $seq_cs,
+ SEQ_QUAL => $seq_qual,
+ SEQ_LEN => length $seq_cs,
+ SEQ => join( "", @seqs ),
+ SCORE_MEAN => sprintf( "%.2f", &Maasha::Calc::mean( \@scores ) ),
+ };
+
+ &put_record( $record, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+
+
+sub script_read_mysql
+{
+ # Martin A. Hansen, May 2008.
+
+ # Read a MySQL query into stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $dbh, $results );
+
+ $options->{ "user" } ||= &Maasha::UCSC::ucsc_get_user();
+ $options->{ "password" } ||= &Maasha::UCSC::ucsc_get_password();
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $dbh = &Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
+
+ $results = &Maasha::SQL::query_hashref_list( $dbh, $options->{ "query" } );
+
+ &Maasha::SQL::disconnect( $dbh );
+
+ map { &put_record( $_ ) } @{ $results };
+}
+
+
+sub script_count_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Count sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $count, $result, $fh );
+
+ $count = 0;
+
+ while ( $record = &get_record( $in ) )
+ {
+ $count++ if $record->{ "SEQ" };
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ $result = { "count_seq" => $count };
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ &put_record( $result, $fh );
+
+ close $fh;
+}
+
+
+sub script_length_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Determine the length of sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $total );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
+ $total += $record->{ "SEQ_LEN" };
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ &put_record( { TOTAL_SEQ_LEN => $total }, $out );
+}
+
+
+sub script_uppercase_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Uppercases sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ $record->{ "SEQ" } = uc $record->{ "SEQ" } if $record->{ "SEQ" };
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_shuffle_seq
+{
+ # Martin A. Hansen, December 2007.
+
+ # Shuffle sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ $record->{ "SEQ" } = &Maasha::Seq::seq_shuffle( $record->{ "SEQ" } ) if $record->{ "SEQ" };
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_analyze_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Analyze sequence composition of sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $analysis );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ $analysis = &Maasha::Seq::seq_analyze( $record->{ "SEQ" } );
+
+ map { $record->{ $_ } = $analysis->{ $_ } } keys %{ $analysis };
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_analyze_tags
+{
+ # Martin A. Hansen, August 2008.
+
+ # Analyze sequence tags in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $analysis, %len_hash, %clone_hash, $clones, $key, $tag_record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ {
+ if ( $record->{ "SEQ_NAME" } =~ /_(\d+)$/ )
+ {
+ $clones = $1;
+
+ $len_hash{ length( $record->{ "SEQ" } ) }++;
+ $clone_hash{ length( $record->{ "SEQ" } ) } += $clones;
+ }
+ }
+ elsif ( $record->{ "Q_ID" } and $record->{ "BED_LEN" } )
+ {
+ if ( $record->{ "Q_ID" } =~ /_(\d+)$/ )
+ {
+ $clones = $1;
+
+ $len_hash{ $record->{ "BED_LEN" } }++;
+ $clone_hash{ $record->{ "BED_LEN" } } += $clones;
+ }
+ }
+ }
+
+ foreach $key ( sort { $a <=> $b } keys %len_hash )
+ {
+ $tag_record->{ "TAG_LEN" } = $key;
+ $tag_record->{ "TAG_COUNT" } = $len_hash{ $key };
+ $tag_record->{ "TAG_CLONES" } = $clone_hash{ $key };
+
+ &put_record( $tag_record, $out );
+ }
+}
+
+
+sub script_complexity_seq
+{
+ # Martin A. Hansen, May 2008.
+
+ # Generates an index calculated as the most common di-residue over
+ # the sequence length for all sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $index );
+
+ while ( $record = &get_record( $in ) )
+ {
+ $record->{ "SEQ_COMPLEXITY" } = sprintf( "%.2f", &Maasha::Seq::seq_complexity( $record->{ "SEQ" } ) ) if $record->{ "SEQ" };
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_oligo_freq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Determine the length of sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, %oligos, @freq_table );
+
+ $options->{ "word_size" } ||= 7;
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ map { $oligos{ $_ }++ } &Maasha::Seq::seq2oligos( \$record->{ "SEQ" }, $options->{ "word_size" } );
+
+ if ( not $options->{ "all" } )
+ {
+ @freq_table = &Maasha::Seq::oligo_freq( \%oligos );
+
+ map { &put_record( $_, $out ) } @freq_table;
+
+ undef %oligos;
+ }
+ }
+
+ &put_record( $record, $out );
+ }
+
+ if ( $options->{ "all" } )
+ {
+ @freq_table = &Maasha::Seq::oligo_freq( \%oligos );
+
+ map { &put_record( $_, $out ) } @freq_table;
+ }
+}
+
+
+sub script_create_weight_matrix
+{
+ # Martin A. Hansen, August 2007.
+
+ # Creates a weight matrix from an alignmnet.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $count, $i, $res, %freq_hash, %res_hash, $freq );
+
+ $count = 0;
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ )
+ {
+ $res = substr $record->{ "SEQ" }, $i, 1;
+
+ $freq_hash{ $i }{ $res }++;
+ $res_hash{ $res } = 1;
+ }
+
+ $count++;
+ }
+ else
+ {
+ &put_record( $record, $out );
+ }
+ }
+
+ foreach $res ( sort keys %res_hash )
+ {
+ undef $record;
+
+ $record->{ "V0" } = $res;
+
+ for ( $i = 0; $i < keys %freq_hash; $i++ )
+ {
+ $freq = $freq_hash{ $i }{ $res } || 0;
+
+ if ( $options->{ "percent" } ) {
+ $freq = sprintf( "%.0f", 100 * $freq / $count ) if $freq > 0;
+ }
+
+ $record->{ "V" . ( $i + 1 ) } = $freq;
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_calc_bit_scores
+{
+ # Martin A. Hansen, March 2007.
+
+ # Calculates the bit scores for each position from an alignmnet in the stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $type, $count, $i, $res, %freq_hash, $bit_max, $bit_height, $bit_diff );
+
+ $count = 0;
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
+
+ for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ )
+ {
+ $res = substr $record->{ "SEQ" }, $i, 1;
+
+ next if $res =~ /-|_|~|\./;
+
+ $freq_hash{ $i }{ $res }++;
+ }
+
+ $count++;
+ }
+ else
+ {
+ &put_record( $record, $out );
+ }
+ }
+
+ undef $record;
+
+ if ( $type eq "protein" ) {
+ $bit_max = 4;
+ } else {
+ $bit_max = 2;
+ }
+
+ for ( $i = 0; $i < keys %freq_hash; $i++ )
+ {
+ $bit_height = &Maasha::Seq::seqlogo_calc_bit_height( $freq_hash{ $i }, $count );
+
+ $bit_diff = $bit_max - $bit_height;
+
+ $record->{ "V" . ( $i ) } = sprintf( "%.2f", $bit_diff );
+ }
+
+ &put_record( $record, $out );
+}
+
+
+sub script_reverse_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Reverse sequence in record.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } ) {
+ $record->{ "SEQ" } = reverse $record->{ "SEQ" };
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_complement_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Complement sequence in record.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $type );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ if ( not $type ) {
+ $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } );
+ }
+
+ if ( $type eq "rna" ) {
+ &Maasha::Seq::rna_comp( \$record->{ "SEQ" } );
+ } elsif ( $type eq "dna" ) {
+ &Maasha::Seq::dna_comp( \$record->{ "SEQ" } );
+ }
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_remove_indels
+{
+ # Martin A. Hansen, August 2007.
+
+ # Remove indels from sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ $record->{ 'SEQ' } =~ tr/-~.//d if $record->{ "SEQ" };
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_transliterate_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Transliterate chars from sequence in record.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $search, $replace, $delete );
+
+ $search = $options->{ "search" } || "";
+ $replace = $options->{ "replace" } || "";
+ $delete = $options->{ "delete" } || "";
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ if ( $search and $replace ) {
+ eval "\$record->{ 'SEQ' } =~ tr/$search/$replace/";
+ } elsif ( $delete ) {
+ eval "\$record->{ 'SEQ' } =~ tr/$delete//d";
+ }
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_transliterate_vals
+{
+ # Martin A. Hansen, April 2008.
+
+ # Transliterate chars from values in record.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $search, $replace, $delete, $key );
+
+ $search = $options->{ "search" } || "";
+ $replace = $options->{ "replace" } || "";
+ $delete = $options->{ "delete" } || "";
+
+ while ( $record = &get_record( $in ) )
+ {
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( exists $record->{ $key } )
+ {
+ if ( $search and $replace ) {
+ eval "\$record->{ $key } =~ tr/$search/$replace/";
+ } elsif ( $delete ) {
+ eval "\$record->{ $key } =~ tr/$delete//d";
+ }
+ }
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_translate_seq
+{
+ # Martin A. Hansen, February 2008.
+
+ # Translate DNA sequence into protein sequence.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $frame, %new_record );
+
+ $options->{ "frames" } ||= [ 1, 2, 3, -1, -2, -3 ];
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ if ( &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) eq "dna" )
+ {
+ foreach $frame ( @{ $options->{ "frames" } } )
+ {
+ %new_record = %{ $record };
+
+ $new_record{ "SEQ" } = &Maasha::Seq::translate( $record->{ "SEQ" }, $frame );
+ $new_record{ "SEQ_LEN" } = length $record->{ "SEQ" };
+ $new_record{ "FRAME" } = $frame;
+
+ &put_record( \%new_record, $out );
+ }
+ }
+ }
+ else
+ {
+ &put_record( $record, $out );
+ }
+ }
+}
+
+
+sub script_extract_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Extract subsequences from sequences in record.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $beg, $end, $len, $record );
+
+ if ( not defined $options->{ "beg" } or $options->{ "beg" } < 0 ) {
+ $beg = 0;
+ } else {
+ $beg = $options->{ "beg" } - 1; # correcting for start offset
+ }
+
+ if ( defined $options->{ "end" } and $options->{ "end" } - 1 < $beg ) {
+ $end = $beg - 1;
+ } elsif ( defined $options->{ "end" } ) {
+ $end = $options->{ "end" } - 1; # correcting for start offset
+ }
+
+ $len = $options->{ "len" };
+
+# print "beg->$beg, end->$end, len->$len\n";
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ if ( defined $beg and defined $end )
+ {
+ if ( $end - $beg + 1 > length $record->{ "SEQ" } ) {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+ } else {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $end - $beg + 1;
+ }
+ }
+ elsif ( defined $beg and defined $len )
+ {
+ if ( $len > length $record->{ "SEQ" } ) {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+ } else {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $len;
+ }
+ }
+ elsif ( defined $beg )
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+ }
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_get_genome_seq
+{
+ # Martin A. Hansen, December 2007.
+
+ # Gets a subsequence from a genome.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $genome_file, $index_file, $index, $fh, $index_head, $index_beg, $index_len, $beg, $len, %lookup_hash, @begs, @lens, $i );
+
+ $options->{ "flank" } ||= 0;
+
+ if ( $options->{ "genome" } )
+ {
+ $genome_file = &Maasha::Config::genome_fasta( $options->{ 'genome' } );
+ $index_file = &Maasha::Config::genome_fasta_index( $options->{ 'genome' } );
+
+ $fh = &Maasha::Common::read_open( $genome_file );
+ $index = &Maasha::Fasta::index_retrieve( $index_file );
+
+ shift @{ $index }; # Get rid of the file size info
+
+ map { $lookup_hash{ $_->[ 0 ] } = [ $_->[ 1 ], $_->[ 2 ] ] } @{ $index };
+
+ if ( exists $lookup_hash{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
+ {
+ ( $index_beg, $index_len ) = @{ $lookup_hash{ $options->{ "chr" } } };
+
+ $beg = $index_beg + $options->{ "beg" } - 1;
+
+ if ( $options->{ "len" } ) {
+ $len = $options->{ "len" };
+ } elsif ( $options->{ "end" } ) {
+ $len = ( $options->{ "end" } - $options->{ "beg" } + 1 );
+ }
+
+ $beg -= $options->{ "flank" };
+ $len += 2 * $options->{ "flank" };
+
+ if ( $beg <= $index_beg )
+ {
+ $len -= $index_beg - $beg;
+ $beg = $index_beg;
+ }
+
+ $len = $index_beg + $index_len - $beg if $beg + $len > $index_beg + $index_len;
+
+ next if $beg > $index_beg + $index_len;
+
+ $record->{ "CHR" } = $options->{ "chr" };
+ $record->{ "CHR_BEG" } = $beg - $index_beg;
+ $record->{ "CHR_END" } = $record->{ "CHR_BEG" } + $len - 1;
+
+ $record->{ "SEQ" } = &Maasha::Common::file_read( $fh, $beg, $len );
+ $record->{ "SEQ_LEN" } = $len;
+
+ &put_record( $record, $out );
+ }
+ }
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $options->{ "genome" } and not $record->{ "SEQ" } )
+ {
+ if ( $record->{ "REC_TYPE" } eq "BED" and exists $lookup_hash{ $record->{ "CHR" } } )
+ {
+ ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "CHR" } } };
+
+ $beg = $record->{ "CHR_BEG" } + $index_beg;
+ $len = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "PSL" and exists $lookup_hash{ $record->{ "S_ID" } } )
+ {
+ ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
+
+ $beg = $record->{ "S_BEG" } + $index_beg;
+ $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BLAST" and exists $lookup_hash{ $record->{ "S_ID" } } )
+ {
+ ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
+
+ $beg = $record->{ "S_BEG" } + $index_beg;
+ $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
+ }
+
+ $beg -= $options->{ "flank" };
+ $len += 2 * $options->{ "flank" };
+
+ if ( $beg <= $index_beg )
+ {
+ $len -= $index_beg - $beg;
+ $beg = $index_beg;
+ }
+
+ $len = $index_beg + $index_len - $beg if $beg + $len > $index_beg + $index_len;
+
+ next if $beg > $index_beg + $index_len;
+
+ $record->{ "CHR_BEG" } = $beg - $index_beg;
+ $record->{ "CHR_END" } = $record->{ "CHR_BEG" } + $len - 1;
+
+ $record->{ "SEQ" } = &Maasha::Common::file_read( $fh, $beg, $len );
+
+ if ( $record->{ "STRAND" } and $record->{ "STRAND" } eq "-" )
+ {
+ &Maasha::Seq::dna_comp( \$record->{ "SEQ" } );
+ $record->{ "SEQ" } = reverse $record->{ "SEQ" };
+ }
+
+ if ( $options->{ "mask" } )
+ {
+ if ( $record->{ "BLOCKCOUNT" } > 1 ) # uppercase hit block segments and lowercase the rest.
+ {
+ $record->{ "SEQ" } = lc $record->{ "SEQ" };
+
+ @begs = split ",", $record->{ "Q_BEGS" };
+ @lens = split ",", $record->{ "BLOCKSIZES" };
+
+ for ( $i = 0; $i < @begs; $i++ ) {
+ substr $record->{ "SEQ" }, $begs[ $i ], $lens[ $i ], uc substr $record->{ "SEQ" }, $begs[ $i ], $lens[ $i ];
+ }
+ }
+ }
+ }
+
+ &put_record( $record, $out );
+ }
+
+ close $fh if $fh;
+}
+
+
+sub script_get_genome_align
+{
+ # Martin A. Hansen, April 2008.
+
+ # Gets a subalignment from a multiple genome alignment.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $maf_track, $align, $align_num, $beg, $end, $len, $entry );
+
+ $options->{ "strand" } ||= "+";
+
+ $align_num = 1;
+
+ $maf_track = &Maasha::Config::maf_track( $options->{ "genome" } );
+
+ if ( $options->{ "chr" } and $options->{ "beg" } and ( $options->{ "end" } or $options->{ "len" } ) )
+ {
+ $beg = $options->{ "beg" } - 1;
+
+ if ( $options->{ "end" } ) {
+ $end = $options->{ "end" };
+ } elsif ( $options->{ "len" } ) {
+ $end = $beg + $options->{ "len" };
+ }
+
+ $align = &Maasha::UCSC::maf_extract( $TMP_DIR, $options->{ "genome" }, $maf_track, $options->{ "chr" }, $beg, $end, $options->{ "strand" } );
+
+ foreach $entry ( @{ $align } )
+ {
+ $entry->{ "ALIGN" } = $align_num;
+ $entry->{ "CHR" } = $record->{ "CHR" };
+ $entry->{ "CHR_BEG" } = $record->{ "CHR_BEG" };
+ $entry->{ "CHR_END" } = $record->{ "CHR_END" };
+ $entry->{ "STRAND" } = $record->{ "STRAND" } || '+';
+ $entry->{ "Q_ID" } = $record->{ "Q_ID" };
+ $entry->{ "SCORE" } = $record->{ "SCORE" };
+
+ &put_record( $entry, $out );
+ }
+ }
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "REC_TYPE" } eq "BED" )
+ {
+ $align = &Maasha::UCSC::maf_extract( $TMP_DIR, $options->{ "genome" }, $maf_track, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $record->{ "STRAND" } );
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "PSL" )
+ {
+ $align = &Maasha::UCSC::maf_extract( $TMP_DIR, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } );
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BLAST" )
+ {
+ $align = &Maasha::UCSC::maf_extract( $TMP_DIR, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } );
+ }
+
+ foreach $entry ( @{ $align } )
+ {
+ $entry->{ "ALIGN" } = $align_num;
+ $entry->{ "CHR" } = $record->{ "CHR" };
+ $entry->{ "CHR_BEG" } = $record->{ "CHR_BEG" };
+ $entry->{ "CHR_END" } = $record->{ "CHR_END" };
+ $entry->{ "STRAND" } = $record->{ "STRAND" };
+ $entry->{ "Q_ID" } = $record->{ "Q_ID" };
+ $entry->{ "SCORE" } = $record->{ "SCORE" };
+
+ &put_record( $entry, $out );
+ }
+
+ $align_num++;
+ }
+}
+
+
+sub script_get_genome_phastcons
+{
+ # Martin A. Hansen, February 2008.
+
+ # Get phastcons scores from genome intervals.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $phastcons_file, $phastcons_index, $index, $fh_phastcons, $scores, $record );
+
+ $options->{ "flank" } ||= 0;
+
+ $phastcons_file = &Maasha::Config::genome_phastcons( $options->{ "genome" } );
+ $phastcons_index = &Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
+
+ $index = &Maasha::UCSC::phastcons_index_retrieve( $phastcons_index );
+ $fh_phastcons = &Maasha::Common::read_open( $phastcons_file );
+
+ if ( defined $options->{ "chr" } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
+ {
+ $options->{ "beg" } -= 1; # request is 1-based
+ $options->{ "end" } -= 1; # request is 1-based
+
+ if ( $options->{ "len" } ) {
+ $options->{ "end" } = $options->{ "beg" } + $options->{ "len" } - 1;
+ }
+
+ $scores = &Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $options->{ "chr" }, $options->{ "beg" }, $options->{ "end" }, $options->{ "flank" } );
+
+ $record->{ "CHR" } = $options->{ "chr" };
+ $record->{ "CHR_BEG" } = $options->{ "beg" } - $options->{ "flank" };
+ $record->{ "CHR_END" } = $options->{ "end" } + $options->{ "flank" };
+
+ $record->{ "PHASTCONS" } = join ",", @{ $scores };
+ $record->{ "PHAST_COUNT" } = scalar @{ $scores }; # DEBUG
+
+ &put_record( $record, $out );
+ }
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "REC_TYPE" } eq "BED" )
+ {
+ $scores = &Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } );
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "PSL" )
+ {
+ $scores = &Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } );
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BLAST" )
+ {
+ $scores = &Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } );
+ }
+
+ $record->{ "PHASTCONS" } = join ",", @{ $scores } if @{ $scores };
+# $record->{ "PHAST_COUNT" } = @{ $scores } if @{ $scores }; # DEBUG
+
+ &put_record( $record, $out );
+ }
+
+ close $fh_phastcons if $fh_phastcons;
+}
+
+
+sub script_fold_seq
+{
+ # Martin A. Hansen, December 2007.
+
+ # Folds sequences in stream into secondary structures.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $type, $struct, $index );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } )
+ {
+ if ( not $type ) {
+ $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } );
+ }
+
+ if ( $type ne "protein" )
+ {
+ ( $struct, $index ) = &Maasha::Seq::fold_struct_rnafold( $record->{ "SEQ" } );
+ $record->{ "SEC_STRUCT" } = $struct;
+ $record->{ "FREE_ENERGY" } = $index;
+ $record->{ "SCORE" } = abs int $index;
+ $record->{ "SIZE" } = length $struct;
+ $record->{ "CONF" } = "1," x $record->{ "SIZE" };
+ }
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_split_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Split a sequence in stream into words.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $new_record, $i, $subseq, %lookup );
+
+ $options->{ "word_size" } ||= 7;
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ {
+ for ( $i = 0; $i < length( $record->{ "SEQ" } ) - $options->{ "word_size" } + 1; $i++ )
+ {
+ $subseq = substr $record->{ "SEQ" }, $i, $options->{ "word_size" };
+
+ if ( $options->{ "uniq" } and not $lookup{ $subseq } )
+ {
+ $new_record->{ "REC_TYPE" } = "SPLIT";
+ $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
+ $new_record->{ "SEQ" } = $subseq;
+
+ &put_record( $new_record, $out );
+
+ $lookup{ $subseq } = 1;
+ }
+ else
+ {
+ $new_record->{ "REC_TYPE" } = "SPLIT";
+ $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
+ $new_record->{ "SEQ" } = $subseq;
+
+ &put_record( $new_record, $out );
+ }
+ }
+ }
+ else
+ {
+ &put_record( $record, $out );
+ }
+ }
+}
+
+
+sub script_split_bed
+{
+ # Martin A. Hansen, June 2008.
+
+ # Split a BED record into overlapping windows.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $new_record, $i );
+
+ $options->{ "window_size" } ||= 20;
+ $options->{ "step_size" } ||= 1;
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
+ {
+ $record->{ "BED_LEN" } = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
+
+ for ( $i = 0; $i < $record->{ "BED_LEN" } - $options->{ "window_size" }; $i += $options->{ "step_size" } )
+ {
+ $new_record->{ "REC_TYPE" } = "BED";
+ $new_record->{ "CHR" } = $record->{ "CHR" };
+ $new_record->{ "CHR_BEG" } = $record->{ "CHR_BEG" } + $i;
+ $new_record->{ "CHR_END" } = $record->{ "CHR_BEG" } + $i + $options->{ "window_size" };
+ $new_record->{ "BED_LEN" } = $options->{ "window_size" };
+ $new_record->{ "Q_ID" } = $record->{ "Q_ID" } . "_$i";
+ $new_record->{ "SCORE" } = $record->{ "SCORE" };
+ $new_record->{ "STRAND" } = $record->{ "STRAND" };
+
+ &put_record( $new_record, $out );
+ }
+ }
+ else
+ {
+ &put_record( $record, $out );
+ }
+ }
+}
+
+
+sub script_align_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Align sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, @entries, $entry );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+ } elsif ( $record->{ "Q_ID" } and $record->{ "SEQ" } ) {
+ push @entries, [ $record->{ "Q_ID" }, $record->{ "SEQ" } ];
+ } else {
+ &put_record( $record, $out );
+ }
+ }
+
+ @entries = &Maasha::Align::align( \@entries );
+
+ foreach $entry ( @entries )
+ {
+ if ( $entry->[ SEQ_NAME ] and $entry->[ SEQ ] )
+ {
+ $record = {
+ ALIGN => 1,
+ SEQ_NAME => $entry->[ SEQ_NAME ],
+ SEQ => $entry->[ SEQ ],
+ };
+
+ &put_record( $record, $out );
+ }
+ }
+}
+
+
+sub script_tile_seq
+{
+ # Martin A. Hansen, February 2008.
+
+ # Using the first sequence in stream as reference, tile
+ # all subsequent sequences based on pairwise alignments.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $first, $ref_entry, @entries );
+
+ $first = 1;
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ {
+ if ( $first )
+ {
+ $ref_entry = [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+
+ $first = 0;
+ }
+ else
+ {
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+ }
+ }
+ else
+ {
+ &put_record( $record, $out );
+ }
+ }
+
+ @entries = &Maasha::Align::align_tile( $ref_entry, \@entries, $options );
+
+ map { &put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ], ALIGN => 1 }, $out ) } @entries;
+}
+
+
+sub script_invert_align
+{
+ # Martin A. Hansen, February 2008.
+
+ # Inverts an alignment showing only non-mathing residues
+ # using the first sequence as reference.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, @entries );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } and $record->{ "ALIGN" } )
+ {
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+ }
+ else
+ {
+ &put_record( $record, $out );
+ }
+ }
+
+ &Maasha::Align::align_invert( \@entries, $options->{ "soft" } );
+
+ map { &put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ], ALIGN => 1 }, $out ) } @entries;
+}
+
+
+sub script_patscan_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Locates patterns in sequences using scan_for_matches.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $genome_file, @args, $arg, $type, $seq_file, $pat_file, $out_file, $fh_in, $fh_out, $record, $patterns, $pattern, $entry, $result, %head_hash, $i );
+
+ if ( $options->{ "patterns" } ) {
+ $patterns = &Maasha::Patscan::parse_patterns( $options->{ "patterns" } );
+ } elsif ( -f $options->{ "patterns_in" } ) {
+ $patterns = &Maasha::Patscan::read_patterns( $options->{ "patterns_in" } );
+ }
+
+ $genome_file = &Maasha::Config::genome_fasta( $options->{ 'genome' } ) if $options->{ 'genome' };
+
+ push @args, "-c" if $options->{ "comp" };
+ push @args, "-m $options->{ 'max_hits' }" if $options->{ 'max_hits' };
+ push @args, "-n $options->{ 'max_misses' }" if $options->{ 'max_hits' };
+
+ $seq_file = "$TMP_DIR/patscan.seq";
+ $pat_file = "$TMP_DIR/patscan.pat";
+ $out_file = "$TMP_DIR/patscan.out";
+
+ $fh_out = &Maasha::Common::write_open( $seq_file );
+
+ $i = 0;
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ" } and $record->{ "SEQ_NAME" } )
+ {
+ $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
+
+ &Maasha::Fasta::put_entry( [ $i, $record->{ "SEQ" } ], $fh_out );
+
+ $head_hash{ $i } = $record->{ "SEQ_NAME" };
+
+ $i++;
+ }
+
+# &put_record( $record, $out );
+ }
+
+ close $fh_out;
+
+ $arg = join " ", @args;
+ $arg .= " -p" if $type eq "protein";
+
+ foreach $pattern ( @{ $patterns } )
+ {
+ $fh_out = &Maasha::Common::write_open( $pat_file );
+
+ print $fh_out "$pattern\n";
+
+ close $fh_out;
+
+ if ( $options->{ 'genome' } ) {
+ `scan_for_matches $arg $pat_file < $genome_file > $out_file`;
+ # &Maasha::Common::run( "scan_for_matches", "$arg $pat_file < $genome_file > $out_file" );
+ } else {
+ `scan_for_matches $arg $pat_file < $seq_file > $out_file`;
+ # &Maasha::Common::run( "scan_for_matches", "$arg $pat_file < $seq_file > $out_file" );
+ }
+
+ $fh_in = &Maasha::Common::read_open( $out_file );
+
+ while ( $entry = &Maasha::Fasta::get_entry( $fh_in ) )
+ {
+ $result = &Maasha::Patscan::parse_scan_result( $entry, $pattern );
+
+ if ( $options->{ 'genome' } )
+ {
+ $result->{ "CHR" } = $result->{ "S_ID" };
+ $result->{ "CHR_BEG" } = $result->{ "S_BEG" };
+ $result->{ "CHR_END" } = $result->{ "S_END" };
+
+ delete $result->{ "S_ID" };
+ delete $result->{ "S_BEG" };
+ delete $result->{ "S_END" };
+ }
+ else
+ {
+ $result->{ "S_ID" } = $head_hash{ $result->{ "S_ID" } };
+ }
+
+ &put_record( $result, $out );
+ }
+
+ close $fh_in;
+ }
+
+ unlink $pat_file;
+ unlink $seq_file;
+ unlink $out_file;
+}
+
+
+sub script_create_blast_db
+{
+ # Martin A. Hansen, September 2007.
+
+ # Creates a NCBI BLAST database with formatdb
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $fh, $seq_type, $path, $record );
+
+ $path = $options->{ "database" };
+
+ $fh = &Maasha::Common::write_open( $path );
+
+ while ( $record = &get_record( $in ) )
+ {
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+
+ if ( $record->{ "SEQ" } and $record->{ "SEQ_NAME" } )
+ {
+ $seq_type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $seq_type;
+
+ &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh );
+ }
+ }
+
+ close $fh;
+
+ if ( $seq_type eq "protein" ) {
+ &Maasha::Common::run( "formatdb", "-p T -i $path -t $options->{ 'database' }" );
+ } else {
+ &Maasha::Common::run( "formatdb", "-p F -i $path -t $options->{ 'database' }" );
+ }
+
+ unlink $path;
+}
+
+
+sub script_blast_seq
+{
+ # Martin A. Hansen, September 2007.
+
+ # BLASTs sequences in stream against a given database.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $genome, $q_type, $s_type, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields );
+
+ $options->{ "e_val" } = 10 if not defined $options->{ "e_val" };
+ $options->{ "filter" } = "F";
+ $options->{ "filter" } = "T" if $options->{ "filter" };
+ $options->{ "cpus" } ||= 1;
+
+ $options->{ "database" } = &Maasha::Config::genome_blast( $options->{ 'genome' } ) if $options->{ 'genome' };
+
+ $tmp_in = "$TMP_DIR/blast_query.seq";
+ $tmp_out = "$TMP_DIR/blast.result";
+
+ $fh_out = &Maasha::Common::write_open( $tmp_in );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ {
+ $q_type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $q_type;
+
+ &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out );
+ }
+
+ &put_record( $record, $out );
+ }
+
+ close $fh_out;
+
+ if ( -f $options->{ 'database' } . ".phr" ) {
+ $s_type = "protein";
+ } else {
+ $s_type = "nucleotide";
+ }
+
+ if ( not $options->{ 'program' } )
+ {
+ if ( $q_type ne "protein" and $s_type ne "protein" ) {
+ $options->{ 'program' } = "blastn";
+ } elsif ( $q_type eq "protein" and $s_type eq "protein" ) {
+ $options->{ 'program' } = "blastp";
+ } elsif ( $q_type ne "protein" and $s_type eq "protein" ) {
+ $options->{ 'program' } = "blastx";
+ } elsif ( $q_type eq "protein" and $s_type ne "protein" ) {
+ $options->{ 'program' } = "tblastn";
+ }
+ }
+
+ &Maasha::Common::run( "blastall", "-p $options->{ 'program' } -e $options->{ 'e_val' } -a $options->{ 'cpus' } -m 8 -i $tmp_in -d $options->{ 'database' } -F $options->{ 'filter' } -o $tmp_out > /dev/null 2>&1", 1 );
+
+ unlink $tmp_in;
+
+ $fh_out = &Maasha::Common::read_open( $tmp_out );
+
+ undef $record;
+
+ while ( $line = <$fh_out> )
+ {
+ chomp $line;
+
+ next if $line =~ /^#/;
+
+ @fields = split /\s+/, $line;
+
+ $record->{ "REC_TYPE" } = "BLAST";
+ $record->{ "Q_ID" } = $fields[ 0 ];
+ $record->{ "S_ID" } = $fields[ 1 ];
+ $record->{ "IDENT" } = $fields[ 2 ];
+ $record->{ "ALIGN_LEN" } = $fields[ 3 ];
+ $record->{ "MISMATCHES" } = $fields[ 4 ];
+ $record->{ "GAPS" } = $fields[ 5 ];
+ $record->{ "Q_BEG" } = $fields[ 6 ] - 1; # BLAST is 1-based
+ $record->{ "Q_END" } = $fields[ 7 ] - 1; # BLAST is 1-based
+ $record->{ "S_BEG" } = $fields[ 8 ] - 1; # BLAST is 1-based
+ $record->{ "S_END" } = $fields[ 9 ] - 1; # BLAST is 1-based
+ $record->{ "E_VAL" } = $fields[ 10 ];
+ $record->{ "BIT_SCORE" } = $fields[ 11 ];
+
+ if ( $record->{ "S_BEG" } > $record->{ "S_END" } )
+ {
+ $record->{ "STRAND" } = '-';
+
+ ( $record->{ "S_BEG" }, $record->{ "S_END" } ) = ( $record->{ "S_END" }, $record->{ "S_BEG" } );
+ }
+ else
+ {
+ $record->{ "STRAND" } = '+';
+ }
+
+ &put_record( $record, $out );
+ }
+
+ close $fh_out;
+
+ unlink $tmp_out;
+}
+
+
+sub script_blat_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # BLATs sequences in stream against a given genome.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $blat_args, $genome_file, $query_file, $fh_in, $fh_out, $type, $record, $result_file, $entries );
+
+ $genome_file = &Maasha::Config::genome_fasta( $options->{ "genome" } );
+
+ $options->{ 'tile_size' } ||= 11;
+ $options->{ 'one_off' } ||= 0;
+ $options->{ 'min_identity' } ||= 90;
+ $options->{ 'min_score' } ||= 0;
+ $options->{ 'step_size' } ||= $options->{ 'tile_size' };
+
+ $blat_args .= " -tileSize=$options->{ 'tile_size' }";
+ $blat_args .= " -oneOff=$options->{ 'one_off' }";
+ $blat_args .= " -minIdentity=$options->{ 'min_identity' }";
+ $blat_args .= " -minScore=$options->{ 'min_score' }";
+ $blat_args .= " -stepSize=$options->{ 'step_size' }";
+ $blat_args .= " -ooc=" . &Maasha::Config::genome_blat_ooc( $options->{ "genome" }, 11 ) if $options->{ 'ooc' };
+
+ $query_file = "$TMP_DIR/blat.seq";
+
+ $fh_out = &Maasha::Common::write_open( $query_file );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ {
+ &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out, 80 );
+ $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
+ }
+
+ &put_record( $record, $out );
+ }
+
+ close $fh_out;
+
+ $blat_args .= " -t=dnax" if $type eq "protein";
+ $blat_args .= " -q=$type";
+
+ $result_file = "$TMP_DIR/blat.psl";
+
+ &Maasha::Common::run( "blat", "$genome_file $query_file $blat_args $result_file > /dev/null 2>&1" );
+
+ unlink $query_file;
+
+ $entries = &Maasha::UCSC::psl_get_entries( $result_file );
+
+ map { &put_record( $_, $out ) } @{ $entries };
+
+ unlink $result_file;
+}
+
+
+sub script_match_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # BLATs sequences in stream against a given genome.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, @entries, $results );
+
+ $options->{ "word_size" } ||= 20;
+ $options->{ "direction" } ||= "both";
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+ }
+
+ &put_record( $record, $out );
+ }
+
+ if ( @entries == 1 )
+ {
+ $results = &Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 0 ] ], $options, $TMP_DIR );
+
+ map { &put_record( $_, $out ) } @{ $results };
+ }
+ elsif ( @entries == 2 )
+ {
+ $results = &Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 1 ] ], $options, $TMP_DIR );
+
+ map { &put_record( $_, $out ) } @{ $results };
+ }
+}
+
+
+sub script_create_vmatch_index
+{
+ # Martin A. Hansen, January 2008.
+
+ # Create a vmatch index from sequences in the stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $file_tmp, $fh_tmp, $type );
+
+ if ( $options->{ "index_name" } )
+ {
+ $file_tmp = $options->{ 'index_name' };
+ $fh_tmp = &Maasha::Common::write_open( $file_tmp );
+ }
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $options->{ "index_name" } and $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ {
+ &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_tmp );
+
+ $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ if ( $options->{ "index_name" } )
+ {
+ close $fh_tmp;
+
+ if ( $type eq "protein" ) {
+ &Maasha::Common::run( "mkvtree", "-db $file_tmp -protein -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
+ } else {
+ &Maasha::Common::run( "mkvtree", "-db $file_tmp -dna -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
+ }
+
+ unlink $file_tmp;
+ }
+}
+
+
+sub script_vmatch_seq
+{
+ # Martin A. Hansen, August 2007.
+
+ # Vmatches sequences in stream against a given genome.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( @index_files, @records, $result_file, $fh_in, $record );
+
+ $options->{ 'count' } = 1 if $options->{ 'max_hits' };
+
+ if ( $options->{ "index_name" } ) {
+ @index_files = $options->{ "index_name" };
+ } else {
+ @index_files = &Maasha::Config::genome_vmatch( $options->{ "genome" } );
+ }
+
+ while ( $record = &get_record( $in ) )
+ {
+ push @records, $record;
+
+ &put_record( $record, $out );
+ }
+
+ $result_file = &Maasha::Match::match_vmatch( $TMP_DIR, \@records, \@index_files, $options );
+
+ undef @records;
+
+ $fh_in = &Maasha::Common::read_open( $result_file );
+
+ while ( $record = &Maasha::Match::vmatch_get_entry( $fh_in ) ) {
+ &put_record( $record, $out );
+ }
+
+ close $fh_in;
+
+ unlink $result_file;
+}
+
+
+sub script_write_fasta
+{
+ # Martin A. Hansen, August 2007.
+
+ # Write FASTA entries from sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $fh );
+
+ $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+ &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh, $options->{ "wrap" } );
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ close $fh;
+}
+
+
+sub script_write_align
+{
+ # Martin A. Hansen, August 2007.
+
+ # Write pretty alignments aligned sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $fh, $record, $align, $old_align, @entries );
+
+ $fh = &write_stream( $options->{ "data_out" } ) ;
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "ALIGN" } and $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ {
+ $align = $record->{ "ALIGN" };
+
+ if ( not $old_align )
+ {
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+
+ $old_align = $align;
+ }
+ elsif ( $align == $old_align )
+ {
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+ }
+ else
+ {
+ if ( scalar( @entries ) == 2 ) {
+ &Maasha::Align::align_print_pairwise( $entries[ 0 ], $entries[ 1 ], $fh, $options->{ "wrap" } );
+ } elsif ( scalar ( @entries ) > 2 ) {
+ &Maasha::Align::align_print_multi( \@entries, $fh, $options->{ "wrap" }, $options->{ "no_ruler" }, $options->{ "no_consensus" } );
+ }
+
+ undef @entries;
+ $old_align = $align;
+ }
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ if ( scalar( @entries ) == 2 ) {
+ &Maasha::Align::align_print_pairwise( $entries[ 0 ], $entries[ 1 ], $fh, $options->{ "wrap" } );
+ } elsif ( scalar ( @entries ) > 2 ) {
+ &Maasha::Align::align_print_multi( \@entries, $fh, $options->{ "wrap" }, $options->{ "no_ruler" }, $options->{ "no_consensus" } );
+ }
+
+ close $fh if $fh;
+}
+
+
+sub script_write_blast
+{
+ # Martin A. Hansen, November 2007.
+
+ # Write data in blast table format (-m8 and 9).
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $fh, $record, $first );
+
+ $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } ) ;
+
+ $first = 1;
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "REC_TYPE" } eq "BLAST" )
+ {
+ if ( $options->{ "comment" } and $first )
+ {
+ print "# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score\n";
+
+ $first = 0;
+ }
+
+ if ( $record->{ "STRAND" } eq "-" ) {
+ ( $record->{ "S_BEG" }, $record->{ "S_END" } ) = ( $record->{ "S_END" }, $record->{ "S_BEG" } );
+ }
+
+ print $fh join( "\t",
+ $record->{ "Q_ID" },
+ $record->{ "S_ID" },
+ $record->{ "IDENT" },
+ $record->{ "ALIGN_LEN" },
+ $record->{ "MISMATCHES" },
+ $record->{ "GAPS" },
+ $record->{ "Q_BEG" } + 1,
+ $record->{ "Q_END" } + 1,
+ $record->{ "S_BEG" } + 1,
+ $record->{ "S_END" } + 1,
+ $record->{ "E_VAL" },
+ $record->{ "BIT_SCORE" }
+ ), "\n";
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ close $fh;
+}
+
+
+sub script_write_tab
+{
+ # Martin A. Hansen, August 2007.
+
+ # Write data as table.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $fh, $record, $key, @keys, @vals, $ok, %no_keys, $A, $B );
+
+ $options->{ "delimit" } ||= "\t";
+
+ map { $no_keys{ $_ } = 1 } @{ $options->{ "no_keys" } };
+
+ $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+
+ while ( $record = &get_record( $in ) )
+ {
+ undef @vals;
+ $ok = 1;
+
+ if ( $options->{ "keys" } )
+ {
+ map { $ok = 0 if not exists $record->{ $_ } } @{ $options->{ "keys" } };
+
+ if ( $ok )
+ {
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( exists $record->{ $key } )
+ {
+ push @keys, $key if $options->{ "comment" };
+ push @vals, $record->{ $key };
+ }
+ }
+ }
+ }
+ else
+ {
+ foreach $key ( sort { $A = $a; $B = $b; $A =~ s/^V(\d+)$/$1/; $B =~ s/^V(\d+)$/$1/; $A <=> $B } keys %{ $record } )
+ {
+ next if exists $no_keys{ $key };
+
+ push @keys, $key if $options->{ "comment" };
+ push @vals, $record->{ $key };
+ }
+ }
+
+ if ( @keys and $options->{ "comment" } )
+ {
+ print $fh "#", join( $options->{ "delimit" }, @keys ), "\n";
+
+ delete $options->{ "comment" };
+ }
+
+ print $fh join( $options->{ "delimit" }, @vals ), "\n" if @vals;
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ close $fh;
+}
+
+
+sub script_write_bed
+{
+ # Martin A. Hansen, August 2007.
+
+ # Write BED format for the UCSC genome browser using records in stream.
+
+ # Crude - needs lots of work!
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $fh, $record, $new_record );
+
+ $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "REC_TYPE" } eq "BED" ) # ---- Hits from BED ----
+ {
+ &Maasha::UCSC::bed_put_entry( $record, $fh, $record->{ "BED_COLS" } );
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "PSL" and $record->{ "S_ID" } =~ /^chr/i ) # ---- Hits from BLAT (PSL) ----
+ {
+ $new_record->{ "CHR" } = $record->{ "S_ID" };
+ $new_record->{ "CHR_BEG" } = $record->{ "S_BEG" };
+ $new_record->{ "CHR_END" } = $record->{ "S_END" };
+ $new_record->{ "Q_ID" } = $record->{ "Q_ID" };
+ $new_record->{ "SCORE" } = $record->{ "SCORE" } || 999;
+ $new_record->{ "STRAND" } = $record->{ "STRAND" };
+
+ &Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } ) # ---- Hits from patscan_seq ----
+ {
+ &Maasha::UCSC::bed_put_entry( $record, $fh, 6 );
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/i ) # ---- Hits from BLAST ----
+ {
+ $new_record->{ "CHR" } = $record->{ "S_ID" };
+ $new_record->{ "CHR_BEG" } = $record->{ "S_BEG" };
+ $new_record->{ "CHR_END" } = $record->{ "S_END" };
+ $new_record->{ "Q_ID" } = $record->{ "Q_ID" };
+ $new_record->{ "SCORE" } = $record->{ "SCORE" } || 999; # or use E_VAL somehow
+ $new_record->{ "STRAND" } = $record->{ "STRAND" };
+
+ &Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and $record->{ "S_ID" } =~ /^chr/i ) # ---- Hits from Vmatch ----
+ {
+ $new_record->{ "CHR" } = $record->{ "S_ID" };
+ $new_record->{ "CHR_BEG" } = $record->{ "S_BEG" };
+ $new_record->{ "CHR_END" } = $record->{ "S_END" };
+ $new_record->{ "Q_ID" } = $record->{ "Q_ID" };
+ $new_record->{ "SCORE" } = $record->{ "SCORE" } || 999; # or use E_VAL somehow
+ $new_record->{ "STRAND" } = $record->{ "STRAND" };
+
+ &Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
+ }
+ elsif ( $record->{ "CHR" } and defined $record->{ "CHR_BEG" } and $record->{ "CHR_END" } ) # ---- Generic data from tables ----
+ {
+ &Maasha::UCSC::bed_put_entry( $record, $fh );
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ close $fh;
+}
+
+
+sub script_write_psl
+{
+ # Martin A. Hansen, August 2007.
+
+ # Write PSL output from stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $fh, $record, @output, $first );
+
+ $first = 1;
+
+ $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+
+ while ( $record = &get_record( $in ) )
+ {
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+
+ if ( $record->{ "REC_TYPE" } and $record->{ "REC_TYPE" } eq "PSL" )
+ {
+ &Maasha::UCSC::psl_put_header( $fh ) if $first;
+ &Maasha::UCSC::psl_put_entry( $record, $fh );
+ $first = 0;
+ }
+ }
+
+ close $fh;
+}
+
+
+sub script_write_2bit
+{
+ # Martin A. Hansen, March 2008.
+
+ # Write sequence entries from stream in 2bit format.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $mask, $tmp_file, $fh_tmp, $fh_in, $fh_out );
+
+ $mask = 1 if not $options->{ "no_mask" };
+
+ $tmp_file = "$TMP_DIR/write_2bit.fna";
+ $fh_tmp = &Maasha::Common::write_open( $tmp_file );
+
+ $fh_out = &write_stream( $options->{ "data_out" } );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+ &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_tmp );
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ close $fh_tmp;
+
+ $fh_in = &Maasha::Common::read_open( $tmp_file );
+
+ &Maasha::TwoBit::fasta2twobit( $fh_in, $fh_out, $mask );
+
+ close $fh_in;
+ close $fh_out;
+
+ unlink $tmp_file;
+}
+
+
+sub script_write_solid
+{
+ # Martin A. Hansen, April 2008.
+
+ # Write di-base encoded Solid sequence from entries in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $fh, $seq_cs );
+
+ $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+ {
+ $seq_cs = &Maasha::Solid::seq2color_space( $record->{ "SEQ" } );
+
+ &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $seq_cs ], $fh, $options->{ "wrap" } );
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ close $fh;
+}
+
+
+sub script_plot_seqlogo
+{
+ # Martin A. Hansen, August 2007.
+
+ # Calculates and writes a sequence logo for alignments.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, @entries, $logo, $fh );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ $logo = &Maasha::Plot::seq_logo( \@entries );
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ print $fh $logo;
+
+ close $fh;
+}
+
+
+sub script_plot_phastcons_profiles
+{
+ # Martin A. Hansen, January 2008.
+
+ # Plots PhastCons profiles.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $phastcons_file, $phastcons_index, $index, $fh_phastcons, $record, $scores, $AoA, $plot, $fh );
+
+ $options->{ "title" } ||= "PhastCons Profiles";
+
+ $phastcons_file = &Maasha::Config::genome_phastcons( $options->{ "genome" } );
+ $phastcons_index = &Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
+
+ $index = &Maasha::UCSC::phastcons_index_retrieve( $phastcons_index );
+ $fh_phastcons = &Maasha::Common::read_open( $phastcons_file );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
+ {
+ $scores = &Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } );
+
+ push @{ $AoA }, [ @{ $scores } ];
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ &Maasha::UCSC::phastcons_normalize( $AoA );
+
+ $AoA = [ [ &Maasha::UCSC::phastcons_mean( $AoA ) ] ] if $options->{ "mean" };
+ $AoA = [ [ &Maasha::UCSC::phastcons_median( $AoA ) ] ] if $options->{ "median" };
+
+ $AoA = &Maasha::Matrix::matrix_flip( $AoA );
+
+ $plot = &Maasha::Plot::lineplot_simple( $AoA, $options, $TMP_DIR );
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ print $fh "$_\n" foreach @{ $plot };
+
+ close $fh;
+}
+
+
+sub script_analyze_bed
+{
+ # Martin A. Hansen, March 2008.
+
+ # Analyze BED entries in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ $record = &Maasha::UCSC::bed_analyze( $record ) if $record->{ "REC_TYPE" } eq "BED";
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_analyze_vals
+{
+ # Martin A. Hansen, August 2007.
+
+ # Analyze values for given keys in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $key, @keys, %key_hash, $analysis, $len );
+
+ map { $key_hash{ $_ } = 1 } @{ $options->{ "keys" } };
+
+ while ( $record = &get_record( $in ) )
+ {
+ foreach $key ( keys %{ $record } )
+ {
+ next if $options->{ "keys" } and not exists $key_hash{ $key };
+
+ $analysis->{ $key }->{ "COUNT" }++;
+
+ if ( &Maasha::Calc::is_a_number( $record->{ $key } ) )
+ {
+ $analysis->{ $key }->{ "TYPE" } = "num";
+ $analysis->{ $key }->{ "SUM" } += $record->{ $key };
+ $analysis->{ $key }->{ "MAX" } = $record->{ $key } if $record->{ $key } > $analysis->{ $key }->{ "MAX" } or not $analysis->{ $key }->{ "MAX" };
+ $analysis->{ $key }->{ "MIN" } = $record->{ $key } if $record->{ $key } < $analysis->{ $key }->{ "MIN" } or not $analysis->{ $key }->{ "MIN" };
+ }
+ else
+ {
+ $len = length $record->{ $key };
+
+ $analysis->{ $key }->{ "TYPE" } = "alph";
+ $analysis->{ $key }->{ "SUM" } += $len;
+ $analysis->{ $key }->{ "MAX" } = $len if $len > $analysis->{ $key }->{ "MAX" } or not $analysis->{ $key }->{ "MAX" };
+ $analysis->{ $key }->{ "MIN" } = $len if $len < $analysis->{ $key }->{ "MIM" } or not $analysis->{ $key }->{ "MIN" };
+ }
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ foreach $key ( keys %{ $analysis } )
+ {
+ $analysis->{ $key }->{ "MEAN" } = sprintf "%.2f", $analysis->{ $key }->{ "SUM" } / $analysis->{ $key }->{ "COUNT" };
+ $analysis->{ $key }->{ "SUM" } = sprintf "%.2f", $analysis->{ $key }->{ "SUN" };
+ }
+
+ my ( $keys, $types, $counts, $mins, $maxs, $sums, $means );
+
+ $keys = "KEY ";
+ $types = "TYPE ";
+ $counts = "COUNT";
+ $mins = "MIN ";
+ $maxs = "MAX ";
+ $sums = "SUM ";
+ $means = "MEAN ";
+
+ if ( $options->{ "keys" } ) {
+ @keys = @{ $options->{ "keys" } };
+ } else {
+ @keys = keys %{ $analysis };
+ }
+
+ foreach $key ( @keys )
+ {
+ $keys .= sprintf "% 15s", $key;
+ $types .= sprintf "% 15s", $analysis->{ $key }->{ "TYPE" };
+ $counts .= sprintf "% 15s", $analysis->{ $key }->{ "COUNT" };
+ $mins .= sprintf "% 15s", $analysis->{ $key }->{ "MIN" };
+ $maxs .= sprintf "% 15s", $analysis->{ $key }->{ "MAX" };
+ $sums .= sprintf "% 15s", $analysis->{ $key }->{ "SUM" };
+ $means .= sprintf "% 15s", $analysis->{ $key }->{ "MEAN" };
+ }
+
+ print $out "$keys\n";
+ print $out "$types\n";
+ print $out "$counts\n";
+ print $out "$mins\n";
+ print $out "$maxs\n";
+ print $out "$sums\n";
+ print $out "$means\n";
+}
+
+
+sub script_head_records
+{
+ # Martin A. Hansen, August 2007.
+
+ # Display the first sequences in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $count );
+
+ $options->{ "num" } ||= 10;
+
+ $count = 0;
+
+ while ( $record = &get_record( $in ) )
+ {
+ $count++;
+
+ &put_record( $record, $out );
+
+ last if $count == $options->{ "num" };
+ }
+}
+
+
+sub script_remove_keys
+{
+ # Martin A. Hansen, August 2007.
+
+ # Remove keys from stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $new_record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $options->{ "keys" } )
+ {
+ map { delete $record->{ $_ } } @{ $options->{ "keys" } };
+ }
+ elsif ( $options->{ "save_keys" } )
+ {
+ map { $new_record->{ $_ } = $record->{ $_ } if exists $record->{ $_ } } @{ $options->{ "save_keys" } };
+
+ $record = $new_record;
+ }
+
+ &put_record( $record, $out ) if keys %{ $record };
+ }
+}
+
+
+sub script_rename_keys
+{
+ # Martin A. Hansen, August 2007.
+
+ # Rename keys in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( exists $record->{ $options->{ "keys" }->[ 0 ] } )
+ {
+ $record->{ $options->{ "keys" }->[ 1 ] } = $record->{ $options->{ "keys" }->[ 0 ] };
+
+ delete $record->{ $options->{ "keys" }->[ 0 ] };
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_uniq_vals
+{
+ # Martin A. Hansen, August 2007.
+
+ # Find unique values in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( %hash, $record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ $options->{ "key" } } )
+ {
+ if ( not $hash{ $record->{ $options->{ "key" } } } and not $options->{ "invert" } )
+ {
+ &put_record( $record, $out );
+
+ $hash{ $record->{ $options->{ "key" } } } = 1;
+ }
+ elsif ( $hash{ $record->{ $options->{ "key" } } } and $options->{ "invert" } )
+ {
+ &put_record( $record, $out );
+ }
+ else
+ {
+ $hash{ $record->{ $options->{ "key" } } } = 1;
+ }
+ }
+ else
+ {
+ &put_record( $record, $out );
+ }
+ }
+}
+
+
+sub script_merge_vals
+{
+ # Martin A. Hansen, August 2007.
+
+ # Rename keys in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, @join, $i );
+
+ $options->{ "delimit" } ||= '_';
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( exists $record->{ $options->{ "keys" }->[ 0 ] } )
+ {
+ @join = $record->{ $options->{ "keys" }->[ 0 ] };
+
+ for ( $i = 1; $i < @{ $options->{ "keys" } }; $i++ ) {
+ push @join, $record->{ $options->{ "keys" }->[ $i ] } if exists $record->{ $options->{ "keys" }->[ $i ] };
+ }
+
+ $record->{ $options->{ "keys" }->[ 0 ] } = join $options->{ "delimit" }, @join;
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_grab
+{
+ # Martin A. Hansen, August 2007.
+
+ # Grab for records in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $patterns, $pattern, $record, $key, $pos, $op, $val, %lookup_hash );
+
+ if ( $options->{ "patterns" } )
+ {
+ $patterns = [ split ",", $options->{ "patterns" } ];
+ }
+ elsif ( -f $options->{ "patterns_in" } )
+ {
+ $patterns = &Maasha::Patscan::read_patterns( $options->{ "patterns_in" } );
+ }
+ elsif ( -f $options->{ "exact_in" } )
+ {
+ $patterns = &Maasha::Patscan::read_patterns( $options->{ "exact_in" } );
+
+ map { $lookup_hash{ $_ } = 1 } @{ $patterns };
+
+ undef $patterns;
+ }
+
+ if ( $options->{ "eval" } )
+ {
+ if ( $options->{ "eval" } =~ /^([^><=! ]+)\s*(>=|<=|>|<|=|!=|eq|ne)\s*(.+)$/ )
+ {
+ $key = $1;
+ $op = $2;
+ $val = $3;
+ }
+ }
+
+ while ( $record = &get_record( $in ) )
+ {
+ $pos = -1;
+
+ if ( %lookup_hash )
+ {
+ if ( $options->{ "keys" } )
+ {
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( exists $lookup_hash{ $record->{ $key } } )
+ {
+ $pos = 1;
+ goto FOUND;
+ }
+ }
+ }
+ else
+ {
+ foreach $key ( keys %{ $record } )
+ {
+ if ( not $options->{ "vals_only" } )
+ {
+ if ( exists $lookup_hash{ $key } )
+ {
+ $pos = 1;
+ goto FOUND;
+ }
+ }
+
+ if ( not $options->{ "keys_only" } )
+ {
+ if ( exists $lookup_hash{ $record->{ $key } } )
+ {
+ $pos = 1;
+ goto FOUND;
+ }
+ }
+ }
+ }
+ }
+ elsif ( $patterns )
+ {
+ foreach $pattern ( @{ $patterns } )
+ {
+ if ( $options->{ "keys" } )
+ {
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ $pos = index $record->{ $key }, $pattern;
+
+ goto FOUND if $pos >= 0;
+ }
+ }
+ else
+ {
+ foreach $key ( keys %{ $record } )
+ {
+ if ( not $options->{ "vals_only" } )
+ {
+ $pos = index $key, $pattern;
+
+ goto FOUND if $pos >= 0;
+ }
+
+ if ( not $options->{ "keys_only" } )
+ {
+ $pos = index $record->{ $key }, $pattern;
+
+ goto FOUND if $pos >= 0;
+ }
+ }
+ }
+ }
+ }
+ elsif ( $options->{ "regex" } )
+ {
+ if ( $options->{ "keys" } )
+ {
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( $options->{ "case_insensitive" } ) {
+ $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/i;
+ } else {
+ $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/;
+ }
+
+ goto FOUND if $pos >= 0;
+ }
+ }
+ else
+ {
+ foreach $key ( keys %{ $record } )
+ {
+ if ( not $options->{ "vals_only" } )
+ {
+ if ( $options->{ "case_insensitive" } ) {
+ $pos = 1 if $key =~ /$options->{'regex'}/i;
+ } else {
+ $pos = 1 if $key =~ /$options->{'regex'}/;
+ }
+
+ goto FOUND if $pos >= 0;
+ }
+
+ if ( not $options->{ "keys_only" } )
+ {
+ if ( $options->{ "case_insensitive" } ) {
+ $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/i;
+ } else {
+ $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/;
+ }
+
+ goto FOUND if $pos >= 0;
+ }
+ }
+ }
+ }
+ elsif ( $options->{ "eval" } )
+ {
+ if ( defined $record->{ $key } )
+ {
+ if ( $op eq "<" and $record->{ $key } < $val ) {
+ $pos = 1 and goto FOUND;
+ } elsif ( $op eq ">" and $record->{ $key } > $val ) {
+ $pos = 1 and goto FOUND;
+ } elsif ( $op eq ">=" and $record->{ $key } >= $val ) {
+ $pos = 1 and goto FOUND;
+ } elsif ( $op eq "<=" and $record->{ $key } <= $val ) {
+ $pos = 1 and goto FOUND;
+ } elsif ( $op eq "=" and $record->{ $key } == $val ) {
+ $pos = 1 and goto FOUND;
+ } elsif ( $op eq "!=" and $record->{ $key } != $val ) {
+ $pos = 1 and goto FOUND;
+ } elsif ( $op eq "eq" and $record->{ $key } eq $val ) {
+ $pos = 1 and goto FOUND;
+ } elsif ( $op eq "ne" and $record->{ $key } ne $val ) {
+ $pos = 1 and goto FOUND;
+ }
+ }
+ }
+
+ FOUND:
+
+ if ( $pos >= 0 and not $options->{ "invert" } ) {
+ &put_record( $record, $out );
+ } elsif ( $pos < 0 and $options->{ "invert" } ) {
+ &put_record( $record, $out );
+ }
+ }
+}
+
+
+sub script_compute
+{
+ # Martin A. Hansen, August 2007.
+
+ # Evaluate extression for records in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $eval_key, $eval_val, $check, @keys );
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $options->{ "eval" } )
+ {
+ if ( $options->{ "eval" } =~ /^(.+)\s*=\s*(.+)$/ )
+ {
+ $eval_key = $1;
+ $eval_val = $2;
+ }
+
+ if ( not $check )
+ {
+ @keys = split /\W+/, $eval_val;
+ @keys = grep { ! /^\d+$/ } @keys;
+
+ $check = 1;
+ }
+
+ map { $eval_val =~ s/$_/$record->{ $_ }/g } @keys;
+
+ $record->{ $eval_key } = eval "$eval_val" or &Maasha::Common::error( "eval failed -> $@" );
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_flip_tab
+{
+ # Martin A. Hansen, June 2008.
+
+ # Flip a table.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $key, $A, $B, @rows, @matrix, $row, $i );
+
+ while ( $record = &get_record( $in ) )
+ {
+ undef @rows;
+
+ foreach $key ( sort { $A = $a; $B = $b; $A =~ s/^V(\d+)$/$1/; $B =~ s/^V(\d+)$/$1/; $A <=> $B } keys %{ $record } )
+ {
+ push @rows, $record->{ $key };
+
+ }
+
+ push @matrix, [ @rows ];
+ }
+
+ undef $record;
+
+ @matrix = &Maasha::Matrix::matrix_flip( \@matrix );
+
+ foreach $row ( @matrix )
+ {
+ for ( $i = 0; $i < @{ $row }; $i++ ) {
+ $record->{ "V$i" } = $row->[ $i ];
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_add_ident
+{
+ # Martin A. Hansen, May 2008.
+
+ # Add a unique identifier to each record in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $key, $prefix, $i );
+
+ $key = $options->{ "key" } || "ID";
+ $prefix = $options->{ "prefix" } || "ID";
+
+ $i = 0;
+
+ while ( $record = &get_record( $in ) )
+ {
+ $record->{ $key } = sprintf( "$prefix%08d", $i );
+
+ &put_record( $record, $out );
+
+ $i++;
+ }
+}
+
+
+sub script_count_records
+{
+ # Martin A. Hansen, August 2007.
+
+ # Count records in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $count, $result, $fh, $line );
+
+ $count = 0;
+
+ if ( $options->{ "no_stream" } )
+ {
+ while ( $line = <$in> )
+ {
+ chomp $line;
+
+ $count++ if $line eq "---";
+ }
+ }
+ else
+ {
+ while ( $record = &get_record( $in ) )
+ {
+ &put_record( $record, $out );
+
+ $count++;
+ }
+ }
+
+ $result = { "count_records" => $count };
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ &put_record( $result, $fh );
+
+ close $fh;
+}
+
+
+sub script_random_records
+{
+ # Martin A. Hansen, August 2007.
+
+ # Pick a number or random records from stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $tmp_file, $fh_out, $fh_in, $count, $i, %rand_hash, $rand, $max );
+
+ $options->{ "num" } ||= 10;
+
+ $tmp_file = "$TMP_DIR/random_records.tmp";
+
+ $fh_out = &Maasha::Common::write_open( $tmp_file );
+
+ $count = 0;
+
+ while ( $record = &get_record( $in ) )
+ {
+ &put_record( $record, $fh_out );
+
+ $count++;
+ }
+
+ close $fh_out;
+
+ $max = 0;
+ $i = 0;
+
+ &Maasha::Common::error( qq(Requested random records > records in stream) ) if $options->{ "num" } > $count;
+
+ while ( $i < $options->{ "num" } )
+ {
+ $rand = int( rand( $count ) );
+
+ if ( not exists $rand_hash{ $rand } )
+ {
+ $rand_hash{ $rand } = 1;
+
+ $max = $rand if $rand > $max;
+
+ $i++;
+ }
+ }
+
+ $fh_in = &Maasha::Common::read_open( $tmp_file );
+
+ $count = 0;
+
+ while ( $record = &get_record( $fh_in ) )
+ {
+ &put_record( $record, $out ) if exists $rand_hash{ $count };
+
+ last if $count == $max;
+
+ $count++;
+ }
+
+ close $fh_in;
+
+ unlink $tmp_file;
+}
+
+
+sub script_sort_records
+{
+ # Martin A. Hansen, August 2007.
+
+ # Sort to sort records according to keys.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( @keys, $key, @sort_cmd, $sort_str, $sort_sub, @records, $record, $i );
+
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( $key =~ s/n$// ) {
+ push @sort_cmd, qq(\$a->{ "$key" } <=> \$b->{ "$key" });
+ } else {
+ push @sort_cmd, qq(\$a->{ "$key" } cmp \$b->{ "$key" });
+ }
+ }
+
+ $sort_str = join " or ", @sort_cmd;
+ $sort_sub = eval "sub { $sort_str }"; # NB security issue!
+
+ while ( $record = &get_record( $in ) ) {
+ push @records, $record;
+ }
+
+ @records = sort $sort_sub @records;
+
+ if ( $options->{ "reverse" } )
+ {
+ for ( $i = scalar @records - 1; $i >= 0; $i-- ) {
+ &put_record( $records[ $i ], $out );
+ }
+ }
+ else
+ {
+ for ( $i = 0; $i < scalar @records; $i++ ) {
+ &put_record( $records[ $i ], $out );
+ }
+ }
+}
+
+
+sub script_count_vals
+{
+ # Martin A. Hansen, August 2007.
+
+ # Count records in stream.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $num, $record, %count_hash, @records, $tmp_file, $fh_out, $fh_in, $cache );
+
+ $tmp_file = "$TMP_DIR/count_cache.tmp";
+
+ $fh_out = &Maasha::Common::write_open( $tmp_file );
+
+ $num = 0;
+
+ while ( $record = &get_record( $in ) )
+ {
+ map { $count_hash{ $_ }{ $record->{ $_ } }++ if exists $record->{ $_ } } @{ $options->{ "keys" } };
+
+ push @records, $record;
+
+ if ( scalar @records > 5_000_000 ) # too many records to hold in memory - use disk cache
+ {
+ map { &put_record( $_, $fh_out ) } @records;
+
+ undef @records;
+
+ $cache = 1;
+ }
+
+ print STDERR "verbose: records read $num\n" if ( $options->{ 'verbose' } and ( $num % 1_000_000 ) == 0 );
+
+ $num++;
+ }
+
+ close $fh_out;
+
+ if ( $cache )
+ {
+ $num = 0;
+
+ $fh_in = &Maasha::Common::read_open( $tmp_file );
+
+ while ( $record = &get_record( $fh_in ) )
+ {
+ map { $record->{ $_ . "_COUNT" } = $count_hash{ $_ }{ $record->{ $_ } } if exists $record->{ $_ } } @{ $options->{ "keys" } };
+
+ &put_record( $record, $out );
+
+ print STDERR "verbose: cache read $num\n" if ( $options->{ 'verbose' } and ( $num % 1_000_000 ) == 0 );
+
+ $num++;
+ }
+
+ close $fh_in;
+ }
+
+ foreach $record ( @records )
+ {
+ map { $record->{ $_ . "_COUNT" } = $count_hash{ $_ }{ $record->{ $_ } } if exists $record->{ $_ } } @{ $options->{ "keys" } };
+
+ &put_record( $record, $out );
+ }
+
+ unlink $tmp_file;
+}
+
+
+sub script_plot_histogram
+{
+ # Martin A. Hansen, September 2007.
+
+ # Plot a simple histogram for a given key using GNU plot.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, %data_hash, $max, @data_list, $i, $result, $fh );
+
+ $options->{ "title" } ||= "Histogram";
+ $options->{ "sort" } ||= "num";
+
+ while ( $record = &get_record( $in ) )
+ {
+ $data_hash{ $record->{ $options->{ "key" } } }++ if $record->{ $options->{ "key" } };
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ if ( $options->{ "sort" } eq "num" ) {
+ map { push @data_list, [ $_, $data_hash{ $_ } ] } sort { $a <=> $b } keys %data_hash;
+ } else {
+ map { push @data_list, [ $_, $data_hash{ $_ } ] } sort keys %data_hash;
+ }
+
+ $result = &Maasha::Plot::histogram_simple( \@data_list, $options );
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ print $fh "$_\n" foreach @{ $result };
+
+ close $fh;
+}
+
+
+sub script_plot_lendist
+{
+ # Martin A. Hansen, August 2007.
+
+ # Plot length distribution using GNU plot.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, %data_hash, $max, @data_list, $i, $result, $fh );
+
+ $options->{ "title" } ||= "Length Distribution";
+
+ while ( $record = &get_record( $in ) )
+ {
+ $data_hash{ $record->{ $options->{ "key" } } }++ if $record->{ $options->{ "key" } };
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ $max = &Maasha::Calc::list_max( [ keys %data_hash ] );
+
+ for ( $i = 0; $i < $max; $i++ ) {
+ push @data_list, [ $i, $data_hash{ $i } || 0 ];
+ }
+
+ $result = &Maasha::Plot::histogram_lendist( \@data_list, $options );
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ print $fh "$_\n" foreach @{ $result };
+
+ close $fh;
+}
+
+
+sub script_plot_chrdist
+{
+ # Martin A. Hansen, August 2007.
+
+ # Plot chromosome distribution using GNU plot.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, %data_hash, @data_list, $elem, $sort_key, $count, $result, $fh );
+
+ $options->{ "title" } ||= "Chromosome Distribution";
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "CHR" } ) { # generic
+ $data_hash{ $record->{ "CHR" } }++;
+ } elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "S_ID" } =~ /^chr/i ) { # patscan
+ $data_hash{ $record->{ "S_ID" } }++;
+ } elsif ( $record->{ "REC_TYPE" } eq "PSL" and $record->{ "S_ID" } =~ /^chr/i ) { # BLAT / PSL
+ $data_hash{ $record->{ "S_ID" } }++;
+ } elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/i ) { # BLAST
+ $data_hash{ $record->{ "S_ID" } }++;
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ foreach $elem ( keys %data_hash )
+ {
+ $sort_key = $elem;
+
+ $sort_key =~ s/chr//i;
+
+ $sort_key =~ s/^X(.*)/99$1/;
+ $sort_key =~ s/^Y(.*)/99$1/;
+ $sort_key =~ s/^Z(.*)/999$1/;
+ $sort_key =~ s/^M(.*)/9999$1/;
+ $sort_key =~ s/^U(.*)/99999$1/;
+
+ $count = $sort_key =~ tr/_//;
+
+ $sort_key =~ s/_.*/"999999" x $count/ex;
+
+ push @data_list, [ $elem, $data_hash{ $elem }, $sort_key ];
+ }
+
+ @data_list = sort { $a->[ 2 ] <=> $b->[ 2 ] } @data_list;
+
+ $result = &Maasha::Plot::histogram_chrdist( \@data_list, $options );
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ print $fh "$_\n" foreach @{ $result };
+
+ close $fh;
+}
+
+
+sub script_plot_karyogram
+{
+ # Martin A. Hansen, August 2007.
+
+ # Plot hits on karyogram.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( %options, $record, @data, $fh, $result, %data_hash );
+
+ $options->{ "genome" } ||= "human";
+ $options->{ "feat_color" } ||= "black";
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
+ {
+ push @{ $data_hash{ $record->{ "CHR" } } }, [ $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "feat_color" } ];
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ $result = &Maasha::Plot::karyogram( \%data_hash, \%options );
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ print $fh $result;
+
+ close $fh;
+}
+
+
+sub script_plot_matches
+{
+ # Martin A. Hansen, August 2007.
+
+ # Plot matches in 2D generating a dotplot.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, @data, $fh, $result, %data_hash );
+
+ $options->{ "direction" } ||= "both";
+
+ while ( $record = &get_record( $in ) )
+ {
+ if ( defined $record->{ "Q_BEG" } and defined $record->{ "S_BEG" } and $record->{ "Q_END" } and $record->{ "S_END" } ) {
+ push @data, $record;
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ $options->{ "title" } ||= "plot_matches";
+ $options->{ "xlabel" } ||= $data[ 0 ]->{ "Q_ID" };
+ $options->{ "ylabel" } ||= $data[ 0 ]->{ "S_ID" };
+
+ $result = &Maasha::Plot::dotplot_matches( \@data, $options, $TMP_DIR );
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ print $fh "$_\n" foreach @{ $result };
+
+ close $fh;
+}
+
+
+sub script_length_vals
+{
+ # Martin A. Hansen, August 2007.
+
+ # Determine the length of the value for given keys.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $key );
+
+ while ( $record = &get_record( $in ) )
+ {
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( $record->{ $key } ) {
+ $record->{ $key . "_LEN" } = length $record->{ $key };
+ }
+ }
+
+ &put_record( $record, $out );
+ }
+}
+
+
+sub script_sum_vals
+{
+ # Martin A. Hansen, August 2007.
+
+ # Calculates the sums for values of given keys.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $key, %sum_hash, $fh );
+
+ while ( $record = &get_record( $in ) )
+ {
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( $record->{ $key } ) {
+ $sum_hash{ $key } += $record->{ $key };
+ }
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ foreach $key ( @{ $options->{ "keys" } } ) {
+ &put_record( { $key . "_SUM" => $sum_hash{ $key } || 0 } , $fh );
+ }
+
+ close $fh;
+}
+
+
+sub script_mean_vals
+{
+ # Martin A. Hansen, August 2007.
+
+ # Calculate the mean of values of given keys.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $key, %sum_hash, %count_hash, $mean, $fh );
+
+ while ( $record = &get_record( $in ) )
+ {
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( $record->{ $key } )
+ {
+ $sum_hash{ $key } += $record->{ $key };
+ $count_hash{ $key }++;
+ }
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( $count_hash{ $key } ) {
+ $mean = sprintf( "%.2f", ( $sum_hash{ $key } / $count_hash{ $key } ) );
+ } else {
+ $mean = "N/A";
+ }
+
+ &put_record( { $key . "_MEAN" => $mean } , $fh );
+ }
+
+ close $fh;
+}
+
+
+sub script_median_vals
+{
+ # Martin A. Hansen, March 2008.
+
+ # Calculate the median values of given keys.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $key, %median_hash, $median, $fh );
+
+ while ( $record = &get_record( $in ) )
+ {
+ foreach $key ( @{ $options->{ "keys" } } ) {
+ push @{ $median_hash{ $key } }, $record->{ $key } if defined $record->{ $key };
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( $median_hash{ $key } ) {
+ $median = &Maasha::Calc::median( $median_hash{ $key } );
+ } else {
+ $median = "N/A";
+ }
+
+ &put_record( { $key . "_MEDIAN" => $median } , $fh );
+ }
+
+ close $fh;
+}
+
+
+sub script_max_vals
+{
+ # Martin A. Hansen, February 2008.
+
+ # Determine the maximum values of given keys.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $key, $fh, %max_hash, $max_record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( $record->{ $key } )
+ {
+ $max_hash{ $key } = $record->{ $key } if $record->{ $key } > $max_hash{ $key };
+ }
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ $max_record->{ $key . "_MAX" } = $max_hash{ $key };
+ }
+
+ &put_record( $max_record, $fh );
+
+ close $fh;
+}
+
+
+sub script_min_vals
+{
+ # Martin A. Hansen, February 2008.
+
+ # Determine the minimum values of given keys.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $key, $fh, %min_hash, $min_record );
+
+ while ( $record = &get_record( $in ) )
+ {
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ if ( defined $record->{ $key } )
+ {
+ if ( exists $min_hash{ $key } ) {
+ $min_hash{ $key } = $record->{ $key } if $record->{ $key } < $min_hash{ $key };
+ } else {
+ $min_hash{ $key } = $record->{ $key };
+ }
+ }
+ }
+
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+ }
+
+ $fh = &write_stream( $options->{ "data_out" } );
+
+ foreach $key ( @{ $options->{ "keys" } } )
+ {
+ $min_record->{ $key . "_MIN" } = $min_hash{ $key };
+ }
+
+ &put_record( $min_record, $fh );
+
+ close $fh;
+}
+
+
+sub script_upload_to_ucsc
+{
+ # Martin A. Hansen, August 2007.
+
+ # Calculate the mean of values of given keys.
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $record, $file, $wib_file, $wig_file, $wib_dir, $fh_in, $fh_out, $i, $first, $format, $args, $type, $columns, $append, %fh_hash,
+ $chr, $beg, $end, $block, $line, $max, $beg_block, $entry, $q_id, $clones );
+
+ $options->{ "short_label" } ||= $options->{ 'table' };
+ $options->{ "long_label" } ||= $options->{ 'table' };
+ $options->{ "group" } ||= $ENV{ "LOGNAME" };
+ $options->{ "priority" } ||= 1;
+ $options->{ "visibility" } ||= "pack";
+ $options->{ "color" } ||= join( ",", int( rand( 255 ) ), int( rand( 255 ) ), int( rand( 255 ) ) );
+ $options->{ "chunk_size" } ||= 10_000_000_000; # Due to 32-bit UCSC compilation really large tables cannot be loaded in one go.
+
+ $file = "$TMP_DIR/ucsc_upload.tmp";
+
+ $append = 0;
+
+ $first = 1;
+
+ $i = 0;
+
+ if ( $options->{ 'wiggle' } )
+ {
+ $options->{ "visibility" } = "full";
+
+ while ( $record = &get_record( $in ) )
+ {
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+
+ $record->{ "CHR" } = $record->{ "S_ID" } if not defined $record->{ "CHR" };
+ $record->{ "CHR_BEG" } = $record->{ "S_BEG" } if not defined $record->{ "CHR_BEG" };
+ $record->{ "CHR_END" } = $record->{ "S_END" } if not defined $record->{ "CHR_END" };
+
+ $fh_hash{ $record->{ "CHR" } } = &Maasha::Common::write_open( "$TMP_DIR/$record->{ 'CHR' }" ) if not exists $fh_hash{ $record->{ "CHR" } };
+
+ $fh_out = $fh_hash{ $record->{ "CHR" } };
+
+ &Maasha::UCSC::bed_put_entry( $record, $fh_out, 5 );
+ }
+
+ map { close $_ } keys %fh_hash;
+
+ $fh_out = &Maasha::Common::write_open( $file );
+
+ foreach $chr ( sort keys %fh_hash )
+ {
+ &Maasha::Common::run( "bedSort", "$TMP_DIR/$chr $TMP_DIR/$chr" );
+
+ $fh_in = &Maasha::Common::read_open( "$TMP_DIR/$chr" );
+
+ undef $block;
+
+ while ( $entry = &Maasha::UCSC::bed_get_entry( $fh_in, 5 ) )
+ {
+ $chr = $entry->{ 'CHR' };
+ $beg = $entry->{ 'CHR_BEG' };
+ $end = $entry->{ 'CHR_END' };
+ $q_id = $entry->{ 'Q_ID' };
+
+ if ( $q_id =~ /_(\d+)$/ ) {
+ $clones = $1;
+ } else {
+ $clones = 1;
+ }
+
+ if ( $block )
+ {
+ if ( $beg > $max )
+ {
+ &Maasha::UCSC::fixedstep_put_entry( $chr, $beg_block, $block, $fh_out );
+ undef $block;
+ }
+ else
+ {
+ for ( $i = $beg - $beg_block; $i < ( $beg - $beg_block ) + ( $end - $beg ); $i++ ) {
+ $block->[ $i ] += $clones;
+ }
+
+ $max = &Maasha::Calc::max( $max, $end );
+ }
+ }
+
+ if ( not $block )
+ {
+ $beg_block = $beg;
+ $max = $end;
+
+ for ( $i = 0; $i < ( $end - $beg ); $i++ ) {
+ $block->[ $i ] += $clones;
+ }
+ }
+ }
+
+ close $fh_in;
+
+ &Maasha::UCSC::fixedstep_put_entry( $chr, $beg_block, $block, $fh_out );
+
+ unlink "$TMP_DIR/$chr";
+ }
+
+ close $fh_out;
+
+ $wig_file = "$options->{ 'table' }.wig";
+ $wib_file = "$options->{ 'table' }.wib";
+
+ $wib_dir = "$ENV{ 'DATA_DIR' }/genomes/$options->{ 'database' }/wib";
+
+ &Maasha::Common::dir_create_if_not_exists( $wib_dir );
+
+ # &Maasha::Common::run( "wigEncode", "$file $wig_file $wib_file > /dev/null 2>&1" );
+
+ `cd $TMP_DIR && wigEncode $file $wig_file $wib_file > /dev/null 2>&1`;
+ &Maasha::Common::run( "mv", "$TMP_DIR/$wib_file $wib_dir" );
+
+ unlink $file;
+
+ $file = $wig_file;
+
+ $format = "WIGGLE";
+ }
+ else
+ {
+ $fh_out = &Maasha::Common::write_open( $file );
+
+ while ( $record = &get_record( $in ) )
+ {
+ &put_record( $record, $out ) if not $options->{ "no_stream" };
+
+ if ( $record->{ "REC_TYPE" } eq "PSL" )
+ {
+ &Maasha::UCSC::psl_put_header( $fh_out ) if $first;
+ &Maasha::UCSC::psl_put_entry( $record, $fh_out );
+
+ $first = 0;
+
+ $format = "PSL" if not $format;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BED" and $record->{ "SEC_STRUCT" } )
+ {
+ # chrom chromStart chromEnd name score strand size secStr conf
+
+ print $fh_out join ( "\t",
+ $record->{ "CHR" },
+ $record->{ "CHR_BEG" },
+ $record->{ "CHR_END" } + 1,
+ $record->{ "Q_ID" },
+ $record->{ "SCORE" },
+ $record->{ "STRAND" },
+ $record->{ "SIZE" },
+ $record->{ "SEC_STRUCT" },
+ $record->{ "CONF" },
+ ), "\n";
+
+ $format = "BED_SS" if not $format;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BED" )
+ {
+ &Maasha::UCSC::bed_put_entry( $record, $fh_out, $record->{ "BED_COLS" } );
+
+ $format = "BED" if not $format;
+ $columns = $record->{ "BED_COLS" } if not $columns;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } )
+ {
+ &Maasha::UCSC::bed_put_entry( $record, $fh_out, 6 );
+
+ $format = "BED" if not $format;
+ $columns = 6 if not $columns;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/ )
+ {
+ $record->{ "CHR" } = $record->{ "S_ID" };
+ $record->{ "CHR_BEG" } = $record->{ "S_BEG" };
+ $record->{ "CHR_END" } = $record->{ "S_END" };
+ $record->{ "SCORE" } = $record->{ "BIT_SCORE" } * 1000;
+
+ $format = "BED" if not $format;
+ $columns = 6 if not $columns;
+
+ &Maasha::UCSC::bed_put_entry( $record, $fh_out );
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and $record->{ "S_ID" } =~ /^chr/i )
+ {
+ $record->{ "CHR" } = $record->{ "S_ID" };
+ $record->{ "CHR_BEG" } = $record->{ "S_BEG" };
+ $record->{ "CHR_END" } = $record->{ "S_END" };
+ $record->{ "SCORE" } = $record->{ "SCORE" } || 999;
+ $record->{ "SCORE" } = int( $record->{ "SCORE" } );
+
+ $format = "BED" if not $format;
+ $columns = 6 if not $columns;
+
+ &Maasha::UCSC::bed_put_entry( $record, $fh_out, 6 );
+ }
+
+ if ( $i == $options->{ "chunk_size" } )
+ {
+ close $fh_out;
+
+ if ( $format eq "BED" ) {
+ &Maasha::UCSC::bed_upload_to_ucsc( $TMP_DIR, $file, $options, $append );
+ } elsif ( $format eq "PSL" ) {
+ &Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
+ }
+
+ unlink $file;
+
+ $first = 1;
+
+ $append = 1;
+
+ $fh_out = &Maasha::Common::write_open( $file );
+ }
+
+ $i++;
+ }
+ }
+
+ close $fh_out;
+
+ if ( exists $options->{ "database" } and $options->{ "table" } )
+ {
+ if ( $format eq "BED" )
+ {
+ $type = "bed $columns";
+
+ &Maasha::UCSC::bed_upload_to_ucsc( $TMP_DIR, $file, $options, $append );
+ }
+ elsif ( $format eq "BED_SS" )
+ {
+ $options->{ "sec_struct" } = 1;
+
+ $type = "sec_struct";
+
+ &Maasha::UCSC::bed_upload_to_ucsc( $TMP_DIR, $file, $options, $append );
+ }
+ elsif ( $format eq "PSL" )
+ {
+ $type = "psl";
+
+ &Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
+ }
+ elsif ( $format eq "WIGGLE" )
+ {
+ $type = "wig 0";
+
+ &Maasha::UCSC::wiggle_upload_to_ucsc( $TMP_DIR, $wib_dir, $file, $options );
+ }
+
+ unlink $file;
+
+ &Maasha::UCSC::update_my_tracks( $options, $type );
+ }
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub read_stream
+{
+ # Martin A. Hansen, July 2007.
+
+ # Opens a stream to STDIN or a file,
+
+ my ( $path, # path - OPTIONAL
+ ) = @_;
+
+ # Returns filehandle.
+
+ my ( $fh );
+
+ if ( not -t STDIN ) {
+ $fh = &Maasha::Common::read_stdin();
+ } elsif ( not $path ) {
+# &Maasha::Common::error( qq(no data stream) );
+ } else {
+ $fh = &Maasha::Common::read_open( $path );
+ }
+
+# $fh->autoflush(1) if $fh;
+
+ return $fh;
+}
+
+
+sub write_stream
+{
+ # Martin A. Hansen, August 2007.
+
+ # Opens a stream to STDOUT or a file.
+
+ my ( $path, # path - OPTIONAL
+ $gzip, # compress data - OPTIONAL
+ ) = @_;
+
+ # Returns filehandle.
+
+ my ( $fh );
+
+ if ( $path ) {
+ $fh = &Maasha::Common::write_open( $path, $gzip );
+ } else {
+ $fh = &Maasha::Common::write_stdout();
+ }
+
+ return $fh;
+}
+
+
+sub get_record
+{
+ # Martin A. Hansen, July 2007.
+
+ # Reads one record at a time and converts that record
+ # to a Perl data structure (a hash) which is returned.
+
+ my ( $fh,
+ ) = @_;
+
+ # Returns data structure.
+
+ my ( $block, @lines, $line, $key, $value, %record );
+
+ local $/ = "\n---\n";
+
+ $block = <$fh>;
+
+ chomp $block;
+
+ return if not defined $block;
+
+ @lines = split "\n", $block;
+
+ foreach $line ( @lines )
+ {
+ ( $key, $value ) = split ": ", $line;
+
+ $record{ $key } = $value;
+ }
+
+ return wantarray ? %record : \%record;
+}
+
+
+sub put_record
+{
+ # Martin A. Hansen, July 2007.
+
+ # Given a Perl datastructure (a hash ref) emits this to STDOUT or a filehandle.
+
+ my ( $data, # data structure
+ $fh, # file handle - OPTIONAL
+ ) = @_;
+
+ # Returns nothing.
+
+ if ( scalar keys %{ $data } )
+ {
+ if ( $fh )
+ {
+ map { print $fh "$_: $data->{ $_ }\n" } keys %{ $data };
+ print $fh "---\n";
+ }
+ else
+ {
+ map { print "$_: $data->{ $_ }\n" } keys %{ $data };
+ print "---\n";
+ }
+ }
+
+ undef $data;
+}
+
+
+sub getopt_files
+{
+ # Martin A. Hansen, November 2007.
+
+ # Extracts files from an explicit GetOpt::Long argument
+ # allowing for the use of glob. E.g.
+ # --data_in=test.fna
+ # --data_in=test.fna,test2.fna
+ # --data_in=*.fna
+ # --data_in=test.fna,/dir/*.fna
+
+ my ( $option, # option from GetOpt::Long
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $elem, @files );
+
+ foreach $elem ( split ",", $option )
+ {
+ if ( -f $elem ) {
+ push @files, $elem;
+ } elsif ( $elem =~ /\*/ ) {
+ push @files, glob( $elem );
+ }
+ }
+
+ return wantarray ? @files : \@files;
+}
+
+
+sub sig_handler
+{
+ # Martin A. Hansen, April 2008.
+
+ # Removes temporary directory and exits gracefully.
+ # This subroutine is meant to be run always as the last
+ # thing even if a script is dies or is interrupted
+ # or killed.
+
+ my ( $sig, # signal from the %SIG
+ ) = @_;
+
+ # print STDERR "signal->$sig<-\n";
+
+ chomp $sig;
+
+ sleep 1;
+
+ if ( -d $TMP_DIR )
+ {
+ if ( $sig =~ /MAASHA_ERROR/ ) {
+ print STDERR "\nProgram '$script' had an error" . " - Please wait for temporary data to be removed\n";
+ } elsif ( $sig eq "INT" ) {
+ print STDERR "\nProgram '$script' interrupted (ctrl-c was pressed)" . " - Please wait for temporary data to be removed\n";
+ } elsif ( $sig eq "TERM" ) {
+ print STDERR "\nProgram '$script' terminated (someone used kill?)" . " - Please wait for temporary data to be removed\n";
+ } else {
+ print STDERR "\nProgram '$script' died->$sig" . " - Please wait for temporary data to be removed\n";
+ }
+
+ # This is a really bad solution, potentially, anyone can include this module and set
+ # the TMP_DIR to point at any dir and thus take out the machine !!!
+
+ &Maasha::Common::dir_remove( $TMP_DIR );
+ }
+
+ exit( 0 );
+}
+
+
+END
+{
+ # This is a really bad solution, potentially, anyone can include this module and set
+ # the TMP_DIR to point at any dir and thus take out the machine !!!
+
+ &Maasha::Common::dir_remove( $TMP_DIR );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+1;
+
+__END__
+
+
+sub script_read_soft
+{
+ # Martin A. Hansen, December 2007.
+
+ # Read soft format.
+ # http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
+
+ my ( $in, # handle to in stream
+ $out, # handle to out stream
+ $options, # options hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $data_in, $file, $num, $records, $record );
+
+ while ( $record = &get_record( $in ) ) {
+ &put_record( $record, $out );
+ }
+
+ $num = 1;
+
+ foreach $file ( @{ $options->{ "files" } } )
+ {
+ $records = &Maasha::NCBI::soft_parse( $file );
+
+ foreach $record ( @{ $records } )
+ {
+ &put_record( $record, $out );
+
+ goto NUM if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+ }
+
+ NUM:
+
+ close $data_in if $data_in;
+}
+++ /dev/null
-package Maasha::Biotools;
-
-
-# Copyright (C) 2007-2008 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-# Routines for manipulation, parsing and emitting of human/machine readable biotool records.
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use strict;
-use Data::Dumper;
-use Getopt::Long qw( :config bundling );
-use Time::HiRes qw( gettimeofday );
-use Storable qw( dclone );
-use Maasha::Config;
-use Maasha::Common;
-use Maasha::Fasta;
-use Maasha::Align;
-use Maasha::Matrix;
-use Maasha::Match;
-use Maasha::EMBL;
-use Maasha::Stockholm;
-use Maasha::Seq;
-use Maasha::Patscan;
-use Maasha::Plot;
-use Maasha::Calc;
-use Maasha::UCSC;
-use Maasha::NCBI;
-use Maasha::GFF;
-use Maasha::TwoBit;
-use Maasha::Solid;
-use Maasha::SQL;
-
-use vars qw( @ISA @EXPORT_OK );
-
-require Exporter;
-
-@ISA = qw( Exporter );
-
-@EXPORT_OK = qw(
- read_stream
- write_stream
- get_record
- put_record
-);
-
-use constant {
- SEQ_NAME => 0,
- SEQ => 1,
-};
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SIGNAL HANDLER <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-$SIG{ '__DIE__' } = \&sig_handler;
-$SIG{ 'INT' } = \&sig_handler;
-$SIG{ 'TERM' } = \&sig_handler;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GLOBALS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my ( $script, $TMP_DIR );
-
-$script = &Maasha::Common::get_scriptname();
-$TMP_DIR = &Maasha::Common::get_tmpdir();
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LOG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my $log_fh = &Maasha::Common::append_open( $ENV{ "LOG_DIR" } . "/biopieces.log" );
-
-$log_fh->autoflush( 1 );
-
-&log( $log_fh, $script, \@ARGV );
-
-close $log_fh;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> RUN SCRIPT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my $t0 = gettimeofday();
-
-&run_script( $script );
-
-my $t1 = gettimeofday();
-
-print STDERR "Program: $script" . ( " " x ( 25 - length( $script ) ) ) . sprintf( "Run time: %.4f\n", ( $t1 - $t0 ) );
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub log
-{
- # Martin A. Hansen, January 2008.
-
- # Log messages to logfile.
-
- my ( $fh, # filehandle to logfile
- $script, # script name
- $argv, # reference to @ARGV
- ) = @_;
-
- # Returns nothing.
-
- my ( $time_stamp, $user );
-
- $time_stamp = &Maasha::Common::time_stamp();
-
- $user = $ENV{ "USER" };
-
- $script = "biopieces" if $script eq "-e";
-
- print $fh "$time_stamp\t$user\t$script ", join( " ", @{ $argv } ), "\n";
-}
-
-
-sub run_script
-{
- # Martin A. Hansen, August 2007.
-
- # Run a specific script.
-
- my ( $script, # script name
- ) = @_;
-
- # Returns nothing.
-
- my ( $options, $in, $out );
-
- &script_list_biotools( $ENV{ 'INST_DIR'} . "/biotools/usage/" ) if $script eq "list_biotools";
-
- &script_print_usage( $ENV{ 'INST_DIR'} . "/biotools/usage/$script" ) if -t STDIN and not @ARGV;
-
- $options = &get_options( $script );
-
- $in = &read_stream( $options->{ "stream_in" } );
- $out = &write_stream( $options->{ "stream_out" } );
-
- if ( $script eq "read_fasta" ) { &script_read_fasta( $in, $out, $options ) }
- elsif ( $script eq "read_align" ) { &script_read_align( $in, $out, $options ) }
- elsif ( $script eq "read_tab" ) { &script_read_tab( $in, $out, $options ) }
- elsif ( $script eq "read_psl" ) { &script_read_psl( $in, $out, $options ) }
- elsif ( $script eq "read_bed" ) { &script_read_bed( $in, $out, $options ) }
- elsif ( $script eq "read_blast_tab" ) { &script_read_blast_tab( $in, $out, $options ) }
- elsif ( $script eq "read_embl" ) { &script_read_embl( $in, $out, $options ) }
- elsif ( $script eq "read_stockholm" ) { &script_read_stockholm( $in, $out, $options ) }
- elsif ( $script eq "read_phastcons" ) { &script_read_phastcons( $in, $out, $options ) }
- elsif ( $script eq "read_soft" ) { &script_read_soft( $in, $out, $options ) }
- elsif ( $script eq "read_gff" ) { &script_read_gff( $in, $out, $options ) }
- elsif ( $script eq "read_2bit" ) { &script_read_2bit( $in, $out, $options ) }
- elsif ( $script eq "read_solexa" ) { &script_read_solexa( $in, $out, $options ) }
- elsif ( $script eq "read_solid" ) { &script_read_solid( $in, $out, $options ) }
- elsif ( $script eq "read_mysql" ) { &script_read_mysql( $in, $out, $options ) }
- elsif ( $script eq "count_seq" ) { &script_count_seq( $in, $out, $options ) }
- elsif ( $script eq "length_seq" ) { &script_length_seq( $in, $out, $options ) }
- elsif ( $script eq "uppercase_seq" ) { &script_uppercase_seq( $in, $out, $options ) }
- elsif ( $script eq "shuffle_seq" ) { &script_shuffle_seq( $in, $out, $options ) }
- elsif ( $script eq "analyze_seq" ) { &script_analyze_seq( $in, $out, $options ) }
- elsif ( $script eq "analyze_tags" ) { &script_analyze_tags( $in, $out, $options ) }
- elsif ( $script eq "complexity_seq" ) { &script_complexity_seq( $in, $out, $options ) }
- elsif ( $script eq "oligo_freq" ) { &script_oligo_freq( $in, $out, $options ) }
- elsif ( $script eq "create_weight_matrix" ) { &script_create_weight_matrix( $in, $out, $options ) }
- elsif ( $script eq "calc_bit_scores" ) { &script_calc_bit_scores( $in, $out, $options ) }
- elsif ( $script eq "reverse_seq" ) { &script_reverse_seq( $in, $out, $options ) }
- elsif ( $script eq "complement_seq" ) { &script_complement_seq( $in, $out, $options ) }
- elsif ( $script eq "remove_indels" ) { &script_remove_indels( $in, $out, $options ) }
- elsif ( $script eq "transliterate_seq" ) { &script_transliterate_seq( $in, $out, $options ) }
- elsif ( $script eq "transliterate_vals" ) { &script_transliterate_vals( $in, $out, $options ) }
- elsif ( $script eq "translate_seq" ) { &script_translate_seq( $in, $out, $options ) }
- elsif ( $script eq "extract_seq" ) { &script_extract_seq( $in, $out, $options ) }
- elsif ( $script eq "get_genome_seq" ) { &script_get_genome_seq( $in, $out, $options ) }
- elsif ( $script eq "get_genome_align" ) { &script_get_genome_align( $in, $out, $options ) }
- elsif ( $script eq "get_genome_phastcons" ) { &script_get_genome_phastcons( $in, $out, $options ) }
- elsif ( $script eq "fold_seq" ) { &script_fold_seq( $in, $out, $options ) }
- elsif ( $script eq "split_seq" ) { &script_split_seq( $in, $out, $options ) }
- elsif ( $script eq "split_bed" ) { &script_split_bed( $in, $out, $options ) }
- elsif ( $script eq "align_seq" ) { &script_align_seq( $in, $out, $options ) }
- elsif ( $script eq "tile_seq" ) { &script_tile_seq( $in, $out, $options ) }
- elsif ( $script eq "invert_align" ) { &script_invert_align( $in, $out, $options ) }
- elsif ( $script eq "patscan_seq" ) { &script_patscan_seq( $in, $out, $options ) }
- elsif ( $script eq "create_blast_db" ) { &script_create_blast_db( $in, $out, $options ) }
- elsif ( $script eq "blast_seq" ) { &script_blast_seq( $in, $out, $options ) }
- elsif ( $script eq "blat_seq" ) { &script_blat_seq( $in, $out, $options ) }
- elsif ( $script eq "match_seq" ) { &script_match_seq( $in, $out, $options ) }
- elsif ( $script eq "create_vmatch_index" ) { &script_create_vmatch_index( $in, $out, $options ) }
- elsif ( $script eq "vmatch_seq" ) { &script_vmatch_seq( $in, $out, $options ) }
- elsif ( $script eq "write_fasta" ) { &script_write_fasta( $in, $out, $options, $options ) }
- elsif ( $script eq "write_align" ) { &script_write_align( $in, $out, $options ) }
- elsif ( $script eq "write_blast" ) { &script_write_blast( $in, $out, $options ) }
- elsif ( $script eq "write_tab" ) { &script_write_tab( $in, $out, $options ) }
- elsif ( $script eq "write_bed" ) { &script_write_bed( $in, $out, $options ) }
- elsif ( $script eq "write_psl" ) { &script_write_psl( $in, $out, $options ) }
- elsif ( $script eq "write_2bit" ) { &script_write_2bit( $in, $out, $options, $options ) }
- elsif ( $script eq "write_solid" ) { &script_write_solid( $in, $out, $options, $options ) }
- elsif ( $script eq "head_records" ) { &script_head_records( $in, $out, $options ) }
- elsif ( $script eq "remove_keys" ) { &script_remove_keys( $in, $out, $options ) }
- elsif ( $script eq "rename_keys" ) { &script_rename_keys( $in, $out, $options ) }
- elsif ( $script eq "uniq_vals" ) { &script_uniq_vals( $in, $out, $options ) }
- elsif ( $script eq "merge_vals" ) { &script_merge_vals( $in, $out, $options ) }
- elsif ( $script eq "grab" ) { &script_grab( $in, $out, $options ) }
- elsif ( $script eq "compute" ) { &script_compute( $in, $out, $options ) }
- elsif ( $script eq "flip_tab" ) { &script_flip_tab( $in, $out, $options ) }
- elsif ( $script eq "add_ident" ) { &script_add_ident( $in, $out, $options ) }
- elsif ( $script eq "count_records" ) { &script_count_records( $in, $out, $options ) }
- elsif ( $script eq "random_records" ) { &script_random_records( $in, $out, $options ) }
- elsif ( $script eq "sort_records" ) { &script_sort_records( $in, $out, $options ) }
- elsif ( $script eq "count_vals" ) { &script_count_vals( $in, $out, $options ) }
- elsif ( $script eq "plot_histogram" ) { &script_plot_histogram( $in, $out, $options ) }
- elsif ( $script eq "plot_lendist" ) { &script_plot_lendist( $in, $out, $options ) }
- elsif ( $script eq "plot_chrdist" ) { &script_plot_chrdist( $in, $out, $options ) }
- elsif ( $script eq "plot_karyogram" ) { &script_plot_karyogram( $in, $out, $options ) }
- elsif ( $script eq "plot_matches" ) { &script_plot_matches( $in, $out, $options ) }
- elsif ( $script eq "plot_seqlogo" ) { &script_plot_seqlogo( $in, $out, $options ) }
- elsif ( $script eq "plot_phastcons_profiles" ) { &script_plot_phastcons_profiles( $in, $out, $options ) }
- elsif ( $script eq "analyze_bed" ) { &script_analyze_bed( $in, $out, $options ) }
- elsif ( $script eq "analyze_vals" ) { &script_analyze_vals( $in, $out, $options ) }
- elsif ( $script eq "length_vals" ) { &script_length_vals( $in, $out, $options ) }
- elsif ( $script eq "sum_vals" ) { &script_sum_vals( $in, $out, $options ) }
- elsif ( $script eq "mean_vals" ) { &script_mean_vals( $in, $out, $options ) }
- elsif ( $script eq "median_vals" ) { &script_median_vals( $in, $out, $options ) }
- elsif ( $script eq "max_vals" ) { &script_max_vals( $in, $out, $options ) }
- elsif ( $script eq "min_vals" ) { &script_min_vals( $in, $out, $options ) }
- elsif ( $script eq "upload_to_ucsc" ) { &script_upload_to_ucsc( $in, $out, $options ) }
-
- close $in if defined $in;
- close $out;
-
- # unset status - missing
- # write log file - missing
-}
-
-
-sub get_options
-{
- # Martin A. Hansen, February 2008.
-
- # Gets options from commandline and checks these vigerously.
-
- my ( $script, # name of script
- ) = @_;
-
- # Returns hash
-
- my ( %options, @options, $opt, @genomes );
-
- if ( $script eq "read_fasta" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
- elsif ( $script eq "read_align" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
- elsif ( $script eq "read_tab" )
- {
- @options = qw(
- data_in|i=s
- delimit|d=s
- cols|c=s
- keys|k=s
- skip|s=s
- num|n=s
- );
- }
- elsif ( $script eq "read_psl" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
- elsif ( $script eq "read_bed" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
- elsif ( $script eq "read_blast_tab" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
- elsif ( $script eq "read_embl" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- keys|k=s
- feats|f=s
- quals|q=s
- );
- }
- elsif ( $script eq "read_stockholm" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
- elsif ( $script eq "read_phastcons" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- min|m=s
- dist|d=s
- threshold|t=f
- gap|g=s
- );
- }
- elsif ( $script eq "read_soft" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
- elsif ( $script eq "read_gff" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- );
- }
- elsif ( $script eq "read_2bit" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- no_mask|N
- );
- }
- elsif ( $script eq "read_solexa" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- quality|q=s
- );
- }
- elsif ( $script eq "read_solid" )
- {
- @options = qw(
- data_in|i=s
- num|n=s
- quality|q=s
- );
- }
- elsif ( $script eq "read_mysql" )
- {
- @options = qw(
- database|d=s
- query|q=s
- user|u=s
- password|p=s
- );
- }
- elsif ( $script eq "count_seq" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- );
- }
- elsif ( $script eq "length_seq" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- );
- }
- elsif ( $script eq "oligo_freq" )
- {
- @options = qw(
- word_size|w=s
- all|a
- );
- }
- elsif ( $script eq "create_weight_matrix" )
- {
- @options = qw(
- percent|p
- );
- }
- elsif ( $script eq "transliterate_seq" )
- {
- @options = qw(
- search|s=s
- replace|r=s
- delete|d=s
- );
- }
- elsif ( $script eq "transliterate_vals" )
- {
- @options = qw(
- keys|k=s
- search|s=s
- replace|r=s
- delete|d=s
- );
- }
- elsif ( $script eq "translate_seq" )
- {
- @options = qw(
- frames|f=s
- );
- }
- elsif ( $script eq "extract_seq" )
- {
- @options = qw(
- beg|b=s
- end|e=s
- len|l=s
- );
- }
- elsif ( $script eq "get_genome_seq" )
- {
- @options = qw(
- genome|g=s
- chr|c=s
- beg|b=s
- end|e=s
- len|l=s
- flank|f=s
- mask|m
- );
- }
- elsif ( $script eq "get_genome_align" )
- {
- @options = qw(
- genome|g=s
- chr|c=s
- beg|b=s
- end|e=s
- len|l=s
- strand|s=s
- );
- }
- elsif ( $script eq "get_genome_phastcons" )
- {
- @options = qw(
- genome|g=s
- chr|c=s
- beg|b=s
- end|e=s
- len|l=s
- flank|f=s
- );
- }
- elsif ( $script eq "split_seq" )
- {
- @options = qw(
- word_size|w=s
- uniq|u
- );
- }
- elsif ( $script eq "split_bed" )
- {
- @options = qw(
- window_size|w=s
- step_size|s=s
- );
- }
- elsif ( $script eq "tile_seq" )
- {
- @options = qw(
- identity|i=s
- supress_indels|s
- );
- }
- elsif ( $script eq "invert_align" )
- {
- @options = qw(
- soft|s
- );
- }
- elsif ( $script eq "patscan_seq" )
- {
- @options = qw(
- patterns|p=s
- patterns_in|P=s
- comp|c
- max_hits|h=s
- max_misses|m=s
- genome|g=s
- );
- }
- elsif ( $script eq "create_blast_db" )
- {
- @options = qw(
- no_stream|x
- database|d=s
- );
- }
- elsif ( $script eq "blast_seq" )
- {
- @options = qw(
- database|d=s
- genome|g=s
- program|p=s
- e_val|e=f
- filter|f
- cpus|c=s
- no_filter|F
- );
- }
- elsif ( $script eq "blat_seq" )
- {
- @options = qw(
- genome|g=s
- tile_size|t=s
- step_size|s=s
- min_identity|m=s
- min_score|M=s
- one_off|o=s
- ooc|c
- );
- }
- elsif ( $script eq "match_seq" )
- {
- @options = qw(
- word_size|w=s
- direction|d=s
- );
- }
- elsif ( $script eq "create_vmatch_index" )
- {
- @options = qw(
- index_name|i=s
- prefix_length|p=s
- no_stream|x
- );
- }
- elsif ( $script eq "vmatch_seq" )
- {
- @options = qw(
- genome|g=s
- index_name|i=s
- count|c
- max_hits|m=s
- hamming_dist|h=s
- edit_dist|e=s
- );
- }
- elsif ( $script eq "write_fasta" )
- {
- @options = qw(
- wrap|w=s
- no_stream|x
- data_out|o=s
- compress|Z
- );
- }
- elsif ( $script eq "write_align" )
- {
- @options = qw(
- wrap|w=s
- no_stream|x
- no_ruler|R
- no_consensus|C
- data_out|o=s
- );
- }
- elsif ( $script eq "write_blast" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- comment|c
- compress|Z
- );
- }
- elsif ( $script eq "write_tab" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- delimit|d=s
- keys|k=s
- no_keys|K=s
- comment|c
- compress|Z
- );
- }
- elsif ( $script eq "write_bed" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- compress|Z
- );
- }
- elsif ( $script eq "write_psl" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- compress|Z
- );
- }
- elsif ( $script eq "write_2bit" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- no_mask|N
- );
- }
- elsif ( $script eq "write_solid" )
- {
- @options = qw(
- wrap|w=s
- no_stream|x
- data_out|o=s
- compress|Z
- );
- }
- elsif ( $script eq "plot_seqlogo" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- );
- }
- elsif ( $script eq "plot_phastcons_profiles" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- genome|g=s
- mean|m
- median|M
- flank|f=s
- terminal|t=s
- title|T=s
- xlabel|X=s
- ylabel|Y=s
- );
- }
- elsif ( $script eq "analyze_vals" )
- {
- @options = qw(
- no_stream|x
- keys|k=s
- );
- }
- elsif ( $script eq "head_records" )
- {
- @options = qw(
- num|n=s
- );
- }
- elsif ( $script eq "remove_keys" )
- {
- @options = qw(
- keys|k=s
- save_keys|K=s
- );
- }
- elsif ( $script eq "rename_keys" )
- {
- @options = qw(
- keys|k=s
- );
- }
- elsif ( $script eq "uniq_vals" )
- {
- @options = qw(
- key|k=s
- invert|i
- );
- }
- elsif ( $script eq "merge_vals" )
- {
- @options = qw(
- keys|k=s
- delimit|d=s
- );
- }
- elsif ( $script eq "grab" )
- {
- @options = qw(
- patterns|p=s
- patterns_in|P=s
- regex|r=s
- eval|e=s
- exact_in|E=s
- invert|i
- case_insensitive|c
- keys|k=s
- keys_only|K
- vals_only|V
- );
- }
- elsif ( $script eq "compute" )
- {
- @options = qw(
- eval|e=s
- );
- }
- elsif ( $script eq "add_ident" )
- {
- @options = qw(
- prefix|p=s
- key|k=s
- );
- }
- elsif ( $script eq "count_records" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- );
- }
- elsif ( $script eq "random_records" )
- {
- @options = qw(
- num|n=s
- );
- }
- elsif ( $script eq "sort_records" )
- {
- @options = qw(
- reverse|r
- keys|k=s
- );
- }
- elsif ( $script eq "count_vals" )
- {
- @options = qw(
- keys|k=s
- );
- }
- elsif ( $script eq "plot_histogram" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- terminal|t=s
- title|T=s
- xlabel|X=s
- ylabel|Y=s
- key|k=s
- sort|s=s
- );
- }
- elsif ( $script eq "plot_lendist" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- terminal|t=s
- title|T=s
- xlabel|X=s
- ylabel|Y=s
- key|k=s
- );
- }
- elsif ( $script eq "plot_chrdist" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- terminal|t=s
- title|T=s
- xlabel|X=s
- ylabel|Y=s
- );
- }
- elsif ( $script eq "plot_karyogram" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- genome|g=s
- feat_color|f=s
- );
- }
- elsif ( $script eq "plot_matches" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- terminal|t=s
- title|T=s
- xlabel|X=s
- ylabel|Y=s
- direction|d=s
- );
- }
- elsif ( $script eq "length_vals" )
- {
- @options = qw(
- keys|k=s
- );
- }
- elsif ( $script eq "sum_vals" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- keys|k=s
- );
- }
- elsif ( $script eq "mean_vals" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- keys|k=s
- );
- }
- elsif ( $script eq "median_vals" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- keys|k=s
- );
- }
- elsif ( $script eq "max_vals" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- keys|k=s
- );
- }
- elsif ( $script eq "min_vals" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- keys|k=s
- );
- }
- elsif ( $script eq "upload_to_ucsc" )
- {
- @options = qw(
- no_stream|x
- database|d=s
- table|t=s
- short_label|s=s
- long_label|l=s
- group|g=s
- priority|p=f
- use_score|u
- visibility|v=s
- wiggle|w
- color|c=s
- chunk_size|C=s
- );
- }
-
- push @options, qw(
- stream_in|I=s
- stream_out|O=s
- verbose
- );
-
-# print STDERR Dumper( \@options );
-
- GetOptions(
- \%options,
- @options,
- );
-
- $options{ "cols" } = [ split ",", $options{ "cols" } ] if defined $options{ "cols" };
- $options{ "keys" } = [ split ",", $options{ "keys" } ] if defined $options{ "keys" };
- $options{ "no_keys" } = [ split ",", $options{ "no_keys" } ] if defined $options{ "no_keys" };
- $options{ "save_keys" } = [ split ",", $options{ "save_keys" } ] if defined $options{ "save_keys" };
- $options{ "quals" } = [ split ",", $options{ "quals" } ] if defined $options{ "quals" };
- $options{ "feats" } = [ split ",", $options{ "feats" } ] if defined $options{ "feats" };
- $options{ "frames" } = [ split ",", $options{ "frames" } ] if defined $options{ "frames" };
-
- # ---- check arguments ----
-
- if ( $options{ 'data_in' } )
- {
- $options{ "files" } = &getopt_files( $options{ 'data_in' } );
-
- &Maasha::Common::error( qq(Argument to --data_in must be a valid file or fileglob expression) ) if scalar @{ $options{ "files" } } == 0;
- }
-
- map { &Maasha::Common::error( qq(Argument to --cols must be a whole numbers - not "$_") ) if $_ !~ /^\d+$/ } @{ $options{ "cols" } } if $options{ "cols" };
-
-# print STDERR Dumper( \%options );
-
- foreach $opt ( keys %options )
- {
- if ( $opt =~ /stream_in|pattern_in|exact_in/ and not -f $options{ $opt } )
- {
- &Maasha::Common::error( qq(Argument to --$opt must be a valid file or fileglob expression - not "$options{ $opt }") );
- }
- elsif ( $opt =~ /beg|end|word_size|wrap|chunk_size|tile_size|len|prefix_length|num|skip|cpus|window_size|step_size/ and $options{ $opt } !~ /^\d+$/ )
- {
- &Maasha::Common::error( qq(Argument to --$opt must be a whole number - not "$options{ $opt }") );
- }
- elsif ( $opt =~ /max_hits|max_hits|max_misses|dist|edit_dist|flank|gap|hamming_dist|priority/ and $options{ $opt } !~ /^-?\d+$/ )
- {
- &Maasha::Common::error( qq(Argument to --$opt must be an integer - not "$options{ $opt }") );
- }
- elsif ( $opt =~ /identity|threshold/ and $options{ $opt } !~ /^-?(?:\d+(?:\.\d*)?|\.\d+)$/ )
- {
- &Maasha::Common::error( qq(Argument to --$opt must be a decimal number - not "$options{ $opt }") );
- }
- elsif ( $opt =~ /e_val/ and $options{ $opt } !~ /^([+-]?)(?=\d|\.\d)\d*(\.\d*)?([Ee]([+-]?\d+))?$/ )
- {
- &Maasha::Common::error( qq(Argument to --$opt must be a float - not "$options{ $opt }") );
- }
- elsif ( $opt =~ /strand/ and $options{ $opt } !~ /^(\+|-)$/ )
- {
- &Maasha::Common::error( qq(Argument to --$opt must be "+" or "-" - not "$options{ $opt }") );
- }
- elsif ( $opt eq "genome" )
- {
- @genomes = &Maasha::Config::genomes();
-
- if ( not grep $options{ $opt }, @genomes ) {
- &Maasha::Common::error( qq(Genome $options{ $opt } not found in "$ENV{ 'INST_DIR' }/conf/genomes.conf") );
- }
- }
- elsif ( $opt eq "terminal" and not $options{ $opt } =~ /^(svg|post|dumb)/ )
- {
- &Maasha::Common::error( qq(Bad --$opt argument "$options{ $opt }") );
- }
- elsif ( $opt eq "table" and $options{ $opt } =~ /-\./ )
- {
- &Maasha::Common::error( qq(Character '$options{ $opt }' is not allowed in table names) );
- }
- }
-
- &Maasha::Common::error( qq(no --database specified) ) if $script eq "create_blast_db" and not $options{ "database" };
- &Maasha::Common::error( qq(no --index_name specified) ) if $script eq "create_vmatch_index" and not $options{ "index_name" };
- &Maasha::Common::error( qq(no --database or --genome specified) ) if $script eq "blast_seq" and not $options{ "genome" } and not $options{ "database" };
- &Maasha::Common::error( qq(both --database and --genome specified) ) if $script eq "blast_seq" and $options{ "genome" } and $options{ "database" };
- &Maasha::Common::error( qq(no --index_name or --genome specified) ) if $script eq "vmatch_seq" and not $options{ "genome" } and not $options{ "index_name" };
- &Maasha::Common::error( qq(both --index and --genome specified) ) if $script eq "vmatch_seq" and $options{ "genome" } and $options{ "index" };
- &Maasha::Common::error( qq(no --genome specified) ) if $script =~ /get_genome_seq|get_genome_align|get_genome_phastcons|blat_seq|plot_phastcons_profiles|plot_karyogram/ and not $options{ "genome" };
- &Maasha::Common::error( qq(no --key specified) ) if $script =~ /plot_lendist|plot_histogram/ and not $options{ "key" };
- &Maasha::Common::error( qq(no --keys speficied) ) if $script =~ /sort_records|count_vals|sum_vals|mean_vals|median_vals|length_vals/ and not $options{ "keys" };
-
- if ( $script eq "upload_to_ucsc" )
- {
- &Maasha::Common::error( qq(no --database specified) ) if not $options{ "database" };
- &Maasha::Common::error( qq(no --table specified) ) if not $options{ "table" };
- }
-
- return wantarray ? %options : \%options;
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SCRIPTS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub script_print_usage
-{
- # Martin A. Hansen, January 2008.
-
- # Retrieves usage information from file and
- # prints this nicely formatted.
-
- my ( $path, # full path to usage file
- ) = @_;
-
- # Returns nothing.
-
- my ( $script, $fh, $line, @lines, @list, %hash, $key );
-
- $script = ( split "/", $path )[ -1 ];
-
- $fh = &Maasha::Common::read_open( $path );
-
- push @list, "Program name";
-
- $hash{ "Program name" } = [ $script ];
-
- while ( $line = <$fh> )
- {
- chomp $line;
-
- $line =~ s/\$script/$script/g;
-
- if ( $line =~ /^([^:]+):\s+(.+)$/ )
- {
- push @list, $1 if not exists $hash{ $1 };
- push @{ $hash{ $1 } }, $2;
- }
- }
-
- close $fh;
-
- print "\n";
-
- foreach $key ( @list )
- {
- if ( scalar @{ $hash{ $key } } == 1 )
- {
- @lines = &Maasha::Common::wrap_line( $hash{ $key }->[ 0 ], 80 );
-
- printf( "%-15s%s\n", "$key:", shift @lines );
-
- map { printf( "%-15s%s\n", "", $_ ) } @lines;
-
- print "\n";
- }
- else
- {
- print "$key:\n";
-
- map { print " $_\n" } @{ $hash{ $key } };
-
- print "\n";
- }
- }
-
- exit;
-}
-
-
-sub script_list_biotools
-{
- # Martin A. Hansen, January 2008.
-
- # Prints the description from the usage for each of the biotools.
-
- my ( $path, # full path to usage directory
- ) = @_;
-
- # Returns nothing.
-
- my ( @files, $file, $fh, $line, @lines, $program );
-
- @files = &Maasha::Common::ls_files( $path );
-
- foreach $file ( sort @files )
- {
- $program = ( split "/", $file )[ -1 ];
-
- $fh = &Maasha::Common::read_open( $file );
-
- while ( $line = <$fh> )
- {
- chomp $line;
-
- if ( $line =~ /^Description:\s+(.+)/ )
- {
- @lines = &Maasha::Common::wrap_line( $1, 60 );
-
- printf( "%-30s%s\n", $program, shift @lines );
-
- map { printf( "%-30s%s\n", "", $_ ) } @lines;
- }
- }
-
- close $fh;
- }
-
- exit;
-}
-
-
-sub script_read_fasta
-{
- # Martin A. Hansen, August 2007.
-
- # Read sequences from FASTA file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file, $data_in, $entry, $num );
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
-
- while ( $entry = &Maasha::Fasta::get_entry( $data_in ) )
- {
- if ( defined $entry->[ SEQ_NAME ] and $entry->[ SEQ ] )
- {
- $record = {
- SEQ_NAME => $entry->[ SEQ_NAME ],
- SEQ => $entry->[ SEQ ],
- SEQ_LEN => length $entry->[ SEQ ],
- };
-
- &put_record( $record, $out );
- }
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_align
-{
- # Martin A. Hansen, August 2007.
-
- # Read aligned sequences from FASTA file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $entry, $record, $file, $data_in, $num );
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
-
- while ( $entry = &Maasha::Fasta::get_entry( $data_in ) )
- {
- if ( $entry->[ SEQ_NAME ] and $entry->[ SEQ ] )
- {
- $record = {
- ALIGN => 1,
- SEQ_NAME => $entry->[ SEQ_NAME ],
- SEQ => $entry->[ SEQ ],
- ALIGN_LEN => length $entry->[ SEQ ],
- };
-
- &put_record( $record, $out );
- }
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_tab
-{
- # Martin A. Hansen, August 2007.
-
- # Read table or table columns from stream or file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $file, $line, @fields, @fields2, $i, $record, $data_in, $skip, $num );
-
- $options->{ 'delimit' } ||= '\s+';
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $skip = $options->{ 'skip' } ||= 0;
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
-
- while ( $line = <$data_in> )
- {
- if ( $skip )
- {
- $skip--;
- next;
- }
-
- next if $line =~ /^#|^$/;
-
- chomp $line;
-
- undef $record;
- undef @fields2;
-
- @fields = split /$options->{'delimit'}/, $line;
-
- if ( $options->{ "cols" } ) {
- map { push @fields2, $fields[ $_ ] } @{ $options->{ "cols" } };
- } else {
- @fields2 = @fields;
- }
-
- for ( $i = 0; $i < @fields2; $i++ )
- {
- if ( $options->{ "keys" }->[ $i ] ) {
- $record->{ $options->{ "keys" }->[ $i ] } = $fields2[ $i ];
- } else {
- $record->{ "V" . $i } = $fields2[ $i ];
- }
- }
-
- &put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_psl
-{
- # Martin A. Hansen, August 2007.
-
- # Read psl table from stream or file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, @files, $file, $entries, $entry, $num );
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $entries = &Maasha::UCSC::psl_get_entries( $file );
-
- foreach $entry ( @{ $entries } )
- {
- &put_record( $entry, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
- }
-
- NUM:
-}
-
-
-sub script_read_bed
-{
- # Martin A. Hansen, August 2007.
-
- # Read bed table from stream or file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $file, $record, $entry, $data_in, $num );
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
-
- while ( $entry = &Maasha::UCSC::bed_get_entry( $data_in ) )
- {
- &put_record( $entry, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_blast_tab
-{
- # Martin A. Hansen, September 2007.
-
- # Read tabular BLAST output from NCBI blast run with -m8 or -m9.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $file, $line, @fields, $strand, $record, $data_in, $num );
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
-
- while ( $line = <$data_in> )
- {
- chomp $line;
-
- next if $line =~ /^#/;
-
- @fields = split /\t/, $line;
-
- $record->{ "REC_TYPE" } = "BLAST";
- $record->{ "Q_ID" } = $fields[ 0 ];
- $record->{ "S_ID" } = $fields[ 1 ];
- $record->{ "IDENT" } = $fields[ 2 ];
- $record->{ "ALIGN_LEN" } = $fields[ 3 ];
- $record->{ "MISMATCHES" } = $fields[ 4 ];
- $record->{ "GAPS" } = $fields[ 5 ];
- $record->{ "Q_BEG" } = $fields[ 6 ] - 1; # BLAST is 1-based
- $record->{ "Q_END" } = $fields[ 7 ] - 1; # BLAST is 1-based
- $record->{ "S_BEG" } = $fields[ 8 ] - 1; # BLAST is 1-based
- $record->{ "S_END" } = $fields[ 9 ] - 1; # BLAST is 1-based
- $record->{ "E_VAL" } = $fields[ 10 ];
- $record->{ "BIT_SCORE" } = $fields[ 11 ];
-
- if ( $record->{ "S_BEG" } > $record->{ "S_END" } )
- {
- $record->{ "STRAND" } = '-';
-
- ( $record->{ "S_BEG" }, $record->{ "S_END" } ) = ( $record->{ "S_END" }, $record->{ "S_BEG" } );
- }
- else
- {
- $record->{ "STRAND" } = '+';
- }
-
- &put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_embl
-{
- # Martin A. Hansen, August 2007.
-
- # Read EMBL format.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( %options2, $file, $data_in, $num, $entry, $record );
-
- map { $options2{ "keys" }{ $_ } = 1 } @{ $options->{ "keys" } };
- map { $options2{ "feats" }{ $_ } = 1 } @{ $options->{ "feats" } };
- map { $options2{ "quals" }{ $_ } = 1 } @{ $options->{ "quals" } };
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
-
- while ( $entry = &Maasha::EMBL::get_embl_entry( $data_in ) )
- {
- $record = &Maasha::EMBL::parse_embl_entry( $entry, \%options2 );
-
- my ( $feat, $feat2, $qual, $qual_val, $record_copy );
-
- $record_copy = dclone $record;
-
- delete $record_copy->{ "FT" };
-
- &put_record( $record_copy, $out );
-
- delete $record_copy->{ "SEQ" };
-
- foreach $feat ( keys %{ $record->{ "FT" } } )
- {
- $record_copy->{ "FEAT_TYPE" } = $feat;
-
- foreach $feat2 ( @{ $record->{ "FT" }->{ $feat } } )
- {
- foreach $qual ( keys %{ $feat2 } )
- {
- $qual_val = join "; ", @{ $feat2->{ $qual } };
-
- $qual =~ s/^_//;
- $qual = uc $qual;
-
- $record_copy->{ $qual } = $qual_val;
- }
-
- &put_record( $record_copy, $out );
- }
- }
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_stockholm
-{
- # Martin A. Hansen, August 2007.
-
- # Read Stockholm format.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $data_in, $file, $num, $entry, $record, $record_anno, $record_align, $key, $seq );
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
-
- while ( $entry = &Maasha::Stockholm::get_stockholm_entry( $data_in ) )
- {
- $record = &Maasha::Stockholm::parse_stockholm_entry( $entry );
-
- undef $record_anno;
-
- foreach $key ( keys %{ $record->{ "GF" } } ) {
- $record_anno->{ $key } = $record->{ "GF" }->{ $key };
- }
-
- $record_anno->{ "ALIGN" } = $num;
-
- &put_record( $record_anno, $out );
-
- foreach $seq ( @{ $record->{ "ALIGN" } } )
- {
- undef $record_align;
-
- $record_align = {
- ALIGN => $num,
- SEQ_NAME => $seq->[ 0 ],
- SEQ => $seq->[ 1 ],
- };
-
- &put_record( $record_align, $out );
- }
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_phastcons
-{
- # Martin A. Hansen, December 2007.
-
- # Read PhastCons format.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $data_in, $file, $num, $entry, @records, $record );
-
- $options->{ "min" } ||= 10;
- $options->{ "dist" } ||= 25;
- $options->{ "threshold" } ||= 0.8;
- $options->{ "gap" } ||= 5;
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
-
- while ( $entry = &Maasha::UCSC::phastcons_get_entry( $data_in ) )
- {
- @records = &Maasha::UCSC::phastcons_parse_entry( $entry, $options );
-
- foreach $record ( @records )
- {
- $record->{ "REC_TYPE" } = "BED";
- $record->{ "BED_LEN" } = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
-
- &put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_soft
-{
- # Martin A. Hansen, December 2007.
-
- # Read soft format.
- # http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $data_in, $file, $num, $records, $record, $soft_index, $fh, @platforms, $plat_table, @samples, $sample, $old_end );
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $soft_index = &Maasha::NCBI::soft_index_file( $file );
-
- $fh = &Maasha::Common::read_open( $file );
-
- @platforms = grep { $_->[ 0 ] =~ /PLATFORM/ } @{ $soft_index };
-
- $plat_table = &Maasha::NCBI::soft_get_platform( $fh, $platforms[ 0 ]->[ 1 ], $platforms[ -1 ]->[ 2 ] );
-
- @samples = grep { $_->[ 0 ] =~ /SAMPLE/ } @{ $soft_index };
-
- $old_end = $platforms[ -1 ]->[ 2 ];
-
- foreach $sample ( @samples )
- {
- $records = &Maasha::NCBI::soft_get_sample( $fh, $plat_table, $sample->[ 1 ] - $old_end - 1, $sample->[ 2 ] - $old_end - 1 );
-
- foreach $record ( @{ $records } )
- {
- &put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- $old_end = $sample->[ 2 ];
- }
-
- close $fh;
- }
-
- NUM:
-
- close $data_in if $data_in;
- close $fh if $fh;
-}
-
-
-sub script_read_gff
-{
- # Martin A. Hansen, February 2008.
-
- # Read soft format.
- # http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $data_in, $file, $fh, $num, $record, $entry );
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $fh = &Maasha::Common::read_open( $file );
-
- while ( $entry = &Maasha::GFF::get_entry( $fh ) )
- {
- &put_record( $entry, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $fh;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_2bit
-{
- # Martin A. Hansen, March 2008.
-
- # Read sequences from 2bit file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file, $data_in, $mask, $toc, $line, $num );
-
- $mask = 1 if not $options->{ "no_mask" };
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
-
- $toc = &Maasha::TwoBit::twobit_get_TOC( $data_in );
-
- foreach $line ( @{ $toc } )
- {
- $record->{ "SEQ_NAME" } = $line->[ 0 ];
- $record->{ "SEQ" } = &Maasha::TwoBit::twobit_get_seq( $data_in, $line->[ 1 ], undef, undef, $mask );
- $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
-
- &put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_solexa
-{
- # Martin A. Hansen, March 2008.
-
- # Read Solexa sequence reads from file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file, $base_name, $data_in, $line, $num, @fields, @seqs, @scores, $i, $seq, $seq_count );
-
- $options->{ "quality" } ||= 20;
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
- $base_name = &Maasha::Common::get_basename( $file );
- $base_name =~ s/\..*//;
-
- $seq_count = 0;
-
- while ( $line = <$data_in> )
- {
- @fields = split /:/, $line;
- @seqs = split //, $fields[ 5 ];
- @scores = split / /, $fields[ -1 ];
-
- for ( $i = 0; $i < @scores; $i++ ) {
- $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $options->{ "quality" };
- }
-
- $seq = join "", @seqs;
-
- $record->{ "SEQ_NAME" } = sprintf( "%s_ID%08d", $base_name, $seq_count );
- $record->{ "SEQ" } = $seq;
- $record->{ "SEQ_LEN" } = length $seq;
- $record->{ "SCORE_MEAN" } = sprintf ( "%.2f", &Maasha::Calc::mean( \@scores ) );
-
- &put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $seq_count++;
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_solid
-{
- # Martin A. Hansen, April 2008.
-
- # Read Solid sequence from file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file, $data_in, $line, $num, $seq_name, $seq_cs, $seq_qual, @scores, @seqs, $i );
-
- $options->{ "quality" } ||= 15;
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $data_in = &Maasha::Common::read_open( $file );
-
- while ( $line = <$data_in> )
- {
- chomp $line;
-
- ( $seq_name, $seq_cs, $seq_qual ) = split /\t/, $line;
-
- @scores = split /,/, $seq_qual;
- @seqs = split //, &Maasha::Solid::color_space2seq( $seq_cs );
-
- for ( $i = 0; $i < @seqs; $i++ ) {
- $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $options->{ "quality" };
- }
-
- $record = {
- SEQ_NAME => $seq_name,
- SEQ_CS => $seq_cs,
- SEQ_QUAL => $seq_qual,
- SEQ_LEN => length $seq_cs,
- SEQ => join( "", @seqs ),
- SCORE_MEAN => sprintf( "%.2f", &Maasha::Calc::mean( \@scores ) ),
- };
-
- &put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
-
-
-sub script_read_mysql
-{
- # Martin A. Hansen, May 2008.
-
- # Read a MySQL query into stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $dbh, $results );
-
- $options->{ "user" } ||= &Maasha::UCSC::ucsc_get_user();
- $options->{ "password" } ||= &Maasha::UCSC::ucsc_get_password();
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $dbh = &Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
-
- $results = &Maasha::SQL::query_hashref_list( $dbh, $options->{ "query" } );
-
- &Maasha::SQL::disconnect( $dbh );
-
- map { &put_record( $_ ) } @{ $results };
-}
-
-
-sub script_count_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Count sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $count, $result, $fh );
-
- $count = 0;
-
- while ( $record = &get_record( $in ) )
- {
- $count++ if $record->{ "SEQ" };
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $result = { "count_seq" => $count };
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- &put_record( $result, $fh );
-
- close $fh;
-}
-
-
-sub script_length_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Determine the length of sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $total );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
- $total += $record->{ "SEQ_LEN" };
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- &put_record( { TOTAL_SEQ_LEN => $total }, $out );
-}
-
-
-sub script_uppercase_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Uppercases sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record );
-
- while ( $record = &get_record( $in ) )
- {
- $record->{ "SEQ" } = uc $record->{ "SEQ" } if $record->{ "SEQ" };
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_shuffle_seq
-{
- # Martin A. Hansen, December 2007.
-
- # Shuffle sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record );
-
- while ( $record = &get_record( $in ) )
- {
- $record->{ "SEQ" } = &Maasha::Seq::seq_shuffle( $record->{ "SEQ" } ) if $record->{ "SEQ" };
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_analyze_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Analyze sequence composition of sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $analysis );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- $analysis = &Maasha::Seq::seq_analyze( $record->{ "SEQ" } );
-
- map { $record->{ $_ } = $analysis->{ $_ } } keys %{ $analysis };
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_analyze_tags
-{
- # Martin A. Hansen, August 2008.
-
- # Analyze sequence tags in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $analysis, %len_hash, %clone_hash, $clones, $key, $tag_record );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
- {
- if ( $record->{ "SEQ_NAME" } =~ /_(\d+)$/ )
- {
- $clones = $1;
-
- $len_hash{ length( $record->{ "SEQ" } ) }++;
- $clone_hash{ length( $record->{ "SEQ" } ) } += $clones;
- }
- }
- elsif ( $record->{ "Q_ID" } and $record->{ "BED_LEN" } )
- {
- if ( $record->{ "Q_ID" } =~ /_(\d+)$/ )
- {
- $clones = $1;
-
- $len_hash{ $record->{ "BED_LEN" } }++;
- $clone_hash{ $record->{ "BED_LEN" } } += $clones;
- }
- }
- }
-
- foreach $key ( sort { $a <=> $b } keys %len_hash )
- {
- $tag_record->{ "TAG_LEN" } = $key;
- $tag_record->{ "TAG_COUNT" } = $len_hash{ $key };
- $tag_record->{ "TAG_CLONES" } = $clone_hash{ $key };
-
- &put_record( $tag_record, $out );
- }
-}
-
-
-sub script_complexity_seq
-{
- # Martin A. Hansen, May 2008.
-
- # Generates an index calculated as the most common di-residue over
- # the sequence length for all sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $index );
-
- while ( $record = &get_record( $in ) )
- {
- $record->{ "SEQ_COMPLEXITY" } = sprintf( "%.2f", &Maasha::Seq::seq_complexity( $record->{ "SEQ" } ) ) if $record->{ "SEQ" };
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_oligo_freq
-{
- # Martin A. Hansen, August 2007.
-
- # Determine the length of sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, %oligos, @freq_table );
-
- $options->{ "word_size" } ||= 7;
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- map { $oligos{ $_ }++ } &Maasha::Seq::seq2oligos( \$record->{ "SEQ" }, $options->{ "word_size" } );
-
- if ( not $options->{ "all" } )
- {
- @freq_table = &Maasha::Seq::oligo_freq( \%oligos );
-
- map { &put_record( $_, $out ) } @freq_table;
-
- undef %oligos;
- }
- }
-
- &put_record( $record, $out );
- }
-
- if ( $options->{ "all" } )
- {
- @freq_table = &Maasha::Seq::oligo_freq( \%oligos );
-
- map { &put_record( $_, $out ) } @freq_table;
- }
-}
-
-
-sub script_create_weight_matrix
-{
- # Martin A. Hansen, August 2007.
-
- # Creates a weight matrix from an alignmnet.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $count, $i, $res, %freq_hash, %res_hash, $freq );
-
- $count = 0;
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ )
- {
- $res = substr $record->{ "SEQ" }, $i, 1;
-
- $freq_hash{ $i }{ $res }++;
- $res_hash{ $res } = 1;
- }
-
- $count++;
- }
- else
- {
- &put_record( $record, $out );
- }
- }
-
- foreach $res ( sort keys %res_hash )
- {
- undef $record;
-
- $record->{ "V0" } = $res;
-
- for ( $i = 0; $i < keys %freq_hash; $i++ )
- {
- $freq = $freq_hash{ $i }{ $res } || 0;
-
- if ( $options->{ "percent" } ) {
- $freq = sprintf( "%.0f", 100 * $freq / $count ) if $freq > 0;
- }
-
- $record->{ "V" . ( $i + 1 ) } = $freq;
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_calc_bit_scores
-{
- # Martin A. Hansen, March 2007.
-
- # Calculates the bit scores for each position from an alignmnet in the stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $type, $count, $i, $res, %freq_hash, $bit_max, $bit_height, $bit_diff );
-
- $count = 0;
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
-
- for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ )
- {
- $res = substr $record->{ "SEQ" }, $i, 1;
-
- next if $res =~ /-|_|~|\./;
-
- $freq_hash{ $i }{ $res }++;
- }
-
- $count++;
- }
- else
- {
- &put_record( $record, $out );
- }
- }
-
- undef $record;
-
- if ( $type eq "protein" ) {
- $bit_max = 4;
- } else {
- $bit_max = 2;
- }
-
- for ( $i = 0; $i < keys %freq_hash; $i++ )
- {
- $bit_height = &Maasha::Seq::seqlogo_calc_bit_height( $freq_hash{ $i }, $count );
-
- $bit_diff = $bit_max - $bit_height;
-
- $record->{ "V" . ( $i ) } = sprintf( "%.2f", $bit_diff );
- }
-
- &put_record( $record, $out );
-}
-
-
-sub script_reverse_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Reverse sequence in record.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } ) {
- $record->{ "SEQ" } = reverse $record->{ "SEQ" };
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_complement_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Complement sequence in record.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $type );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- if ( not $type ) {
- $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } );
- }
-
- if ( $type eq "rna" ) {
- &Maasha::Seq::rna_comp( \$record->{ "SEQ" } );
- } elsif ( $type eq "dna" ) {
- &Maasha::Seq::dna_comp( \$record->{ "SEQ" } );
- }
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_remove_indels
-{
- # Martin A. Hansen, August 2007.
-
- # Remove indels from sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record );
-
- while ( $record = &get_record( $in ) )
- {
- $record->{ 'SEQ' } =~ tr/-~.//d if $record->{ "SEQ" };
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_transliterate_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Transliterate chars from sequence in record.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $search, $replace, $delete );
-
- $search = $options->{ "search" } || "";
- $replace = $options->{ "replace" } || "";
- $delete = $options->{ "delete" } || "";
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- if ( $search and $replace ) {
- eval "\$record->{ 'SEQ' } =~ tr/$search/$replace/";
- } elsif ( $delete ) {
- eval "\$record->{ 'SEQ' } =~ tr/$delete//d";
- }
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_transliterate_vals
-{
- # Martin A. Hansen, April 2008.
-
- # Transliterate chars from values in record.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $search, $replace, $delete, $key );
-
- $search = $options->{ "search" } || "";
- $replace = $options->{ "replace" } || "";
- $delete = $options->{ "delete" } || "";
-
- while ( $record = &get_record( $in ) )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( exists $record->{ $key } )
- {
- if ( $search and $replace ) {
- eval "\$record->{ $key } =~ tr/$search/$replace/";
- } elsif ( $delete ) {
- eval "\$record->{ $key } =~ tr/$delete//d";
- }
- }
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_translate_seq
-{
- # Martin A. Hansen, February 2008.
-
- # Translate DNA sequence into protein sequence.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $frame, %new_record );
-
- $options->{ "frames" } ||= [ 1, 2, 3, -1, -2, -3 ];
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- if ( &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) eq "dna" )
- {
- foreach $frame ( @{ $options->{ "frames" } } )
- {
- %new_record = %{ $record };
-
- $new_record{ "SEQ" } = &Maasha::Seq::translate( $record->{ "SEQ" }, $frame );
- $new_record{ "SEQ_LEN" } = length $record->{ "SEQ" };
- $new_record{ "FRAME" } = $frame;
-
- &put_record( \%new_record, $out );
- }
- }
- }
- else
- {
- &put_record( $record, $out );
- }
- }
-}
-
-
-sub script_extract_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Extract subsequences from sequences in record.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $beg, $end, $len, $record );
-
- if ( not defined $options->{ "beg" } or $options->{ "beg" } < 0 ) {
- $beg = 0;
- } else {
- $beg = $options->{ "beg" } - 1; # correcting for start offset
- }
-
- if ( defined $options->{ "end" } and $options->{ "end" } - 1 < $beg ) {
- $end = $beg - 1;
- } elsif ( defined $options->{ "end" } ) {
- $end = $options->{ "end" } - 1; # correcting for start offset
- }
-
- $len = $options->{ "len" };
-
-# print "beg->$beg, end->$end, len->$len\n";
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- if ( defined $beg and defined $end )
- {
- if ( $end - $beg + 1 > length $record->{ "SEQ" } ) {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
- } else {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $end - $beg + 1;
- }
- }
- elsif ( defined $beg and defined $len )
- {
- if ( $len > length $record->{ "SEQ" } ) {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
- } else {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $len;
- }
- }
- elsif ( defined $beg )
- {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
- }
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_get_genome_seq
-{
- # Martin A. Hansen, December 2007.
-
- # Gets a subsequence from a genome.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $genome_file, $index_file, $index, $fh, $index_head, $index_beg, $index_len, $beg, $len, %lookup_hash, @begs, @lens, $i );
-
- $options->{ "flank" } ||= 0;
-
- if ( $options->{ "genome" } )
- {
- $genome_file = &Maasha::Config::genome_fasta( $options->{ 'genome' } );
- $index_file = &Maasha::Config::genome_fasta_index( $options->{ 'genome' } );
-
- $fh = &Maasha::Common::read_open( $genome_file );
- $index = &Maasha::Fasta::index_retrieve( $index_file );
-
- shift @{ $index }; # Get rid of the file size info
-
- map { $lookup_hash{ $_->[ 0 ] } = [ $_->[ 1 ], $_->[ 2 ] ] } @{ $index };
-
- if ( exists $lookup_hash{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
- {
- ( $index_beg, $index_len ) = @{ $lookup_hash{ $options->{ "chr" } } };
-
- $beg = $index_beg + $options->{ "beg" } - 1;
-
- if ( $options->{ "len" } ) {
- $len = $options->{ "len" };
- } elsif ( $options->{ "end" } ) {
- $len = ( $options->{ "end" } - $options->{ "beg" } + 1 );
- }
-
- $beg -= $options->{ "flank" };
- $len += 2 * $options->{ "flank" };
-
- if ( $beg <= $index_beg )
- {
- $len -= $index_beg - $beg;
- $beg = $index_beg;
- }
-
- $len = $index_beg + $index_len - $beg if $beg + $len > $index_beg + $index_len;
-
- next if $beg > $index_beg + $index_len;
-
- $record->{ "CHR" } = $options->{ "chr" };
- $record->{ "CHR_BEG" } = $beg - $index_beg;
- $record->{ "CHR_END" } = $record->{ "CHR_BEG" } + $len - 1;
-
- $record->{ "SEQ" } = &Maasha::Common::file_read( $fh, $beg, $len );
- $record->{ "SEQ_LEN" } = $len;
-
- &put_record( $record, $out );
- }
- }
-
- while ( $record = &get_record( $in ) )
- {
- if ( $options->{ "genome" } and not $record->{ "SEQ" } )
- {
- if ( $record->{ "REC_TYPE" } eq "BED" and exists $lookup_hash{ $record->{ "CHR" } } )
- {
- ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "CHR" } } };
-
- $beg = $record->{ "CHR_BEG" } + $index_beg;
- $len = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
- }
- elsif ( $record->{ "REC_TYPE" } eq "PSL" and exists $lookup_hash{ $record->{ "S_ID" } } )
- {
- ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
-
- $beg = $record->{ "S_BEG" } + $index_beg;
- $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
- }
- elsif ( $record->{ "REC_TYPE" } eq "BLAST" and exists $lookup_hash{ $record->{ "S_ID" } } )
- {
- ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
-
- $beg = $record->{ "S_BEG" } + $index_beg;
- $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
- }
-
- $beg -= $options->{ "flank" };
- $len += 2 * $options->{ "flank" };
-
- if ( $beg <= $index_beg )
- {
- $len -= $index_beg - $beg;
- $beg = $index_beg;
- }
-
- $len = $index_beg + $index_len - $beg if $beg + $len > $index_beg + $index_len;
-
- next if $beg > $index_beg + $index_len;
-
- $record->{ "CHR_BEG" } = $beg - $index_beg;
- $record->{ "CHR_END" } = $record->{ "CHR_BEG" } + $len - 1;
-
- $record->{ "SEQ" } = &Maasha::Common::file_read( $fh, $beg, $len );
-
- if ( $record->{ "STRAND" } and $record->{ "STRAND" } eq "-" )
- {
- &Maasha::Seq::dna_comp( \$record->{ "SEQ" } );
- $record->{ "SEQ" } = reverse $record->{ "SEQ" };
- }
-
- if ( $options->{ "mask" } )
- {
- if ( $record->{ "BLOCKCOUNT" } > 1 ) # uppercase hit block segments and lowercase the rest.
- {
- $record->{ "SEQ" } = lc $record->{ "SEQ" };
-
- @begs = split ",", $record->{ "Q_BEGS" };
- @lens = split ",", $record->{ "BLOCKSIZES" };
-
- for ( $i = 0; $i < @begs; $i++ ) {
- substr $record->{ "SEQ" }, $begs[ $i ], $lens[ $i ], uc substr $record->{ "SEQ" }, $begs[ $i ], $lens[ $i ];
- }
- }
- }
- }
-
- &put_record( $record, $out );
- }
-
- close $fh if $fh;
-}
-
-
-sub script_get_genome_align
-{
- # Martin A. Hansen, April 2008.
-
- # Gets a subalignment from a multiple genome alignment.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $maf_track, $align, $align_num, $beg, $end, $len, $entry );
-
- $options->{ "strand" } ||= "+";
-
- $align_num = 1;
-
- $maf_track = &Maasha::Config::maf_track( $options->{ "genome" } );
-
- if ( $options->{ "chr" } and $options->{ "beg" } and ( $options->{ "end" } or $options->{ "len" } ) )
- {
- $beg = $options->{ "beg" } - 1;
-
- if ( $options->{ "end" } ) {
- $end = $options->{ "end" };
- } elsif ( $options->{ "len" } ) {
- $end = $beg + $options->{ "len" };
- }
-
- $align = &Maasha::UCSC::maf_extract( $TMP_DIR, $options->{ "genome" }, $maf_track, $options->{ "chr" }, $beg, $end, $options->{ "strand" } );
-
- foreach $entry ( @{ $align } )
- {
- $entry->{ "ALIGN" } = $align_num;
- $entry->{ "CHR" } = $record->{ "CHR" };
- $entry->{ "CHR_BEG" } = $record->{ "CHR_BEG" };
- $entry->{ "CHR_END" } = $record->{ "CHR_END" };
- $entry->{ "STRAND" } = $record->{ "STRAND" } || '+';
- $entry->{ "Q_ID" } = $record->{ "Q_ID" };
- $entry->{ "SCORE" } = $record->{ "SCORE" };
-
- &put_record( $entry, $out );
- }
- }
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "REC_TYPE" } eq "BED" )
- {
- $align = &Maasha::UCSC::maf_extract( $TMP_DIR, $options->{ "genome" }, $maf_track, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $record->{ "STRAND" } );
- }
- elsif ( $record->{ "REC_TYPE" } eq "PSL" )
- {
- $align = &Maasha::UCSC::maf_extract( $TMP_DIR, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } );
- }
- elsif ( $record->{ "REC_TYPE" } eq "BLAST" )
- {
- $align = &Maasha::UCSC::maf_extract( $TMP_DIR, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } );
- }
-
- foreach $entry ( @{ $align } )
- {
- $entry->{ "ALIGN" } = $align_num;
- $entry->{ "CHR" } = $record->{ "CHR" };
- $entry->{ "CHR_BEG" } = $record->{ "CHR_BEG" };
- $entry->{ "CHR_END" } = $record->{ "CHR_END" };
- $entry->{ "STRAND" } = $record->{ "STRAND" };
- $entry->{ "Q_ID" } = $record->{ "Q_ID" };
- $entry->{ "SCORE" } = $record->{ "SCORE" };
-
- &put_record( $entry, $out );
- }
-
- $align_num++;
- }
-}
-
-
-sub script_get_genome_phastcons
-{
- # Martin A. Hansen, February 2008.
-
- # Get phastcons scores from genome intervals.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $phastcons_file, $phastcons_index, $index, $fh_phastcons, $scores, $record );
-
- $options->{ "flank" } ||= 0;
-
- $phastcons_file = &Maasha::Config::genome_phastcons( $options->{ "genome" } );
- $phastcons_index = &Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
-
- $index = &Maasha::UCSC::phastcons_index_retrieve( $phastcons_index );
- $fh_phastcons = &Maasha::Common::read_open( $phastcons_file );
-
- if ( defined $options->{ "chr" } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
- {
- $options->{ "beg" } -= 1; # request is 1-based
- $options->{ "end" } -= 1; # request is 1-based
-
- if ( $options->{ "len" } ) {
- $options->{ "end" } = $options->{ "beg" } + $options->{ "len" } - 1;
- }
-
- $scores = &Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $options->{ "chr" }, $options->{ "beg" }, $options->{ "end" }, $options->{ "flank" } );
-
- $record->{ "CHR" } = $options->{ "chr" };
- $record->{ "CHR_BEG" } = $options->{ "beg" } - $options->{ "flank" };
- $record->{ "CHR_END" } = $options->{ "end" } + $options->{ "flank" };
-
- $record->{ "PHASTCONS" } = join ",", @{ $scores };
- $record->{ "PHAST_COUNT" } = scalar @{ $scores }; # DEBUG
-
- &put_record( $record, $out );
- }
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "REC_TYPE" } eq "BED" )
- {
- $scores = &Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } );
- }
- elsif ( $record->{ "REC_TYPE" } eq "PSL" )
- {
- $scores = &Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } );
- }
- elsif ( $record->{ "REC_TYPE" } eq "BLAST" )
- {
- $scores = &Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } );
- }
-
- $record->{ "PHASTCONS" } = join ",", @{ $scores } if @{ $scores };
-# $record->{ "PHAST_COUNT" } = @{ $scores } if @{ $scores }; # DEBUG
-
- &put_record( $record, $out );
- }
-
- close $fh_phastcons if $fh_phastcons;
-}
-
-
-sub script_fold_seq
-{
- # Martin A. Hansen, December 2007.
-
- # Folds sequences in stream into secondary structures.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $type, $struct, $index );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } )
- {
- if ( not $type ) {
- $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } );
- }
-
- if ( $type ne "protein" )
- {
- ( $struct, $index ) = &Maasha::Seq::fold_struct_rnafold( $record->{ "SEQ" } );
- $record->{ "SEC_STRUCT" } = $struct;
- $record->{ "FREE_ENERGY" } = $index;
- $record->{ "SCORE" } = abs int $index;
- $record->{ "SIZE" } = length $struct;
- $record->{ "CONF" } = "1," x $record->{ "SIZE" };
- }
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_split_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Split a sequence in stream into words.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $new_record, $i, $subseq, %lookup );
-
- $options->{ "word_size" } ||= 7;
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
- {
- for ( $i = 0; $i < length( $record->{ "SEQ" } ) - $options->{ "word_size" } + 1; $i++ )
- {
- $subseq = substr $record->{ "SEQ" }, $i, $options->{ "word_size" };
-
- if ( $options->{ "uniq" } and not $lookup{ $subseq } )
- {
- $new_record->{ "REC_TYPE" } = "SPLIT";
- $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
- $new_record->{ "SEQ" } = $subseq;
-
- &put_record( $new_record, $out );
-
- $lookup{ $subseq } = 1;
- }
- else
- {
- $new_record->{ "REC_TYPE" } = "SPLIT";
- $new_record->{ "SEQ_NAME" } = $record->{ "SEQ_NAME" } . "[" . ( $i + 1 ) . "-" . ( $i + $options->{ "word_size" } ) . "]";
- $new_record->{ "SEQ" } = $subseq;
-
- &put_record( $new_record, $out );
- }
- }
- }
- else
- {
- &put_record( $record, $out );
- }
- }
-}
-
-
-sub script_split_bed
-{
- # Martin A. Hansen, June 2008.
-
- # Split a BED record into overlapping windows.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $new_record, $i );
-
- $options->{ "window_size" } ||= 20;
- $options->{ "step_size" } ||= 1;
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
- {
- $record->{ "BED_LEN" } = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
-
- for ( $i = 0; $i < $record->{ "BED_LEN" } - $options->{ "window_size" }; $i += $options->{ "step_size" } )
- {
- $new_record->{ "REC_TYPE" } = "BED";
- $new_record->{ "CHR" } = $record->{ "CHR" };
- $new_record->{ "CHR_BEG" } = $record->{ "CHR_BEG" } + $i;
- $new_record->{ "CHR_END" } = $record->{ "CHR_BEG" } + $i + $options->{ "window_size" };
- $new_record->{ "BED_LEN" } = $options->{ "window_size" };
- $new_record->{ "Q_ID" } = $record->{ "Q_ID" } . "_$i";
- $new_record->{ "SCORE" } = $record->{ "SCORE" };
- $new_record->{ "STRAND" } = $record->{ "STRAND" };
-
- &put_record( $new_record, $out );
- }
- }
- else
- {
- &put_record( $record, $out );
- }
- }
-}
-
-
-sub script_align_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Align sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, @entries, $entry );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
- push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
- } elsif ( $record->{ "Q_ID" } and $record->{ "SEQ" } ) {
- push @entries, [ $record->{ "Q_ID" }, $record->{ "SEQ" } ];
- } else {
- &put_record( $record, $out );
- }
- }
-
- @entries = &Maasha::Align::align( \@entries );
-
- foreach $entry ( @entries )
- {
- if ( $entry->[ SEQ_NAME ] and $entry->[ SEQ ] )
- {
- $record = {
- ALIGN => 1,
- SEQ_NAME => $entry->[ SEQ_NAME ],
- SEQ => $entry->[ SEQ ],
- };
-
- &put_record( $record, $out );
- }
- }
-}
-
-
-sub script_tile_seq
-{
- # Martin A. Hansen, February 2008.
-
- # Using the first sequence in stream as reference, tile
- # all subsequent sequences based on pairwise alignments.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $first, $ref_entry, @entries );
-
- $first = 1;
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
- {
- if ( $first )
- {
- $ref_entry = [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
-
- $first = 0;
- }
- else
- {
- push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
- }
- }
- else
- {
- &put_record( $record, $out );
- }
- }
-
- @entries = &Maasha::Align::align_tile( $ref_entry, \@entries, $options );
-
- map { &put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ], ALIGN => 1 }, $out ) } @entries;
-}
-
-
-sub script_invert_align
-{
- # Martin A. Hansen, February 2008.
-
- # Inverts an alignment showing only non-mathing residues
- # using the first sequence as reference.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, @entries );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } and $record->{ "ALIGN" } )
- {
- push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
- }
- else
- {
- &put_record( $record, $out );
- }
- }
-
- &Maasha::Align::align_invert( \@entries, $options->{ "soft" } );
-
- map { &put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ], ALIGN => 1 }, $out ) } @entries;
-}
-
-
-sub script_patscan_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Locates patterns in sequences using scan_for_matches.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $genome_file, @args, $arg, $type, $seq_file, $pat_file, $out_file, $fh_in, $fh_out, $record, $patterns, $pattern, $entry, $result, %head_hash, $i );
-
- if ( $options->{ "patterns" } ) {
- $patterns = &Maasha::Patscan::parse_patterns( $options->{ "patterns" } );
- } elsif ( -f $options->{ "patterns_in" } ) {
- $patterns = &Maasha::Patscan::read_patterns( $options->{ "patterns_in" } );
- }
-
- $genome_file = &Maasha::Config::genome_fasta( $options->{ 'genome' } ) if $options->{ 'genome' };
-
- push @args, "-c" if $options->{ "comp" };
- push @args, "-m $options->{ 'max_hits' }" if $options->{ 'max_hits' };
- push @args, "-n $options->{ 'max_misses' }" if $options->{ 'max_hits' };
-
- $seq_file = "$TMP_DIR/patscan.seq";
- $pat_file = "$TMP_DIR/patscan.pat";
- $out_file = "$TMP_DIR/patscan.out";
-
- $fh_out = &Maasha::Common::write_open( $seq_file );
-
- $i = 0;
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ" } and $record->{ "SEQ_NAME" } )
- {
- $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
-
- &Maasha::Fasta::put_entry( [ $i, $record->{ "SEQ" } ], $fh_out );
-
- $head_hash{ $i } = $record->{ "SEQ_NAME" };
-
- $i++;
- }
-
-# &put_record( $record, $out );
- }
-
- close $fh_out;
-
- $arg = join " ", @args;
- $arg .= " -p" if $type eq "protein";
-
- foreach $pattern ( @{ $patterns } )
- {
- $fh_out = &Maasha::Common::write_open( $pat_file );
-
- print $fh_out "$pattern\n";
-
- close $fh_out;
-
- if ( $options->{ 'genome' } ) {
- `scan_for_matches $arg $pat_file < $genome_file > $out_file`;
- # &Maasha::Common::run( "scan_for_matches", "$arg $pat_file < $genome_file > $out_file" );
- } else {
- `scan_for_matches $arg $pat_file < $seq_file > $out_file`;
- # &Maasha::Common::run( "scan_for_matches", "$arg $pat_file < $seq_file > $out_file" );
- }
-
- $fh_in = &Maasha::Common::read_open( $out_file );
-
- while ( $entry = &Maasha::Fasta::get_entry( $fh_in ) )
- {
- $result = &Maasha::Patscan::parse_scan_result( $entry, $pattern );
-
- if ( $options->{ 'genome' } )
- {
- $result->{ "CHR" } = $result->{ "S_ID" };
- $result->{ "CHR_BEG" } = $result->{ "S_BEG" };
- $result->{ "CHR_END" } = $result->{ "S_END" };
-
- delete $result->{ "S_ID" };
- delete $result->{ "S_BEG" };
- delete $result->{ "S_END" };
- }
- else
- {
- $result->{ "S_ID" } = $head_hash{ $result->{ "S_ID" } };
- }
-
- &put_record( $result, $out );
- }
-
- close $fh_in;
- }
-
- unlink $pat_file;
- unlink $seq_file;
- unlink $out_file;
-}
-
-
-sub script_create_blast_db
-{
- # Martin A. Hansen, September 2007.
-
- # Creates a NCBI BLAST database with formatdb
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $fh, $seq_type, $path, $record );
-
- $path = $options->{ "database" };
-
- $fh = &Maasha::Common::write_open( $path );
-
- while ( $record = &get_record( $in ) )
- {
- &put_record( $record, $out ) if not $options->{ "no_stream" };
-
- if ( $record->{ "SEQ" } and $record->{ "SEQ_NAME" } )
- {
- $seq_type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $seq_type;
-
- &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh );
- }
- }
-
- close $fh;
-
- if ( $seq_type eq "protein" ) {
- &Maasha::Common::run( "formatdb", "-p T -i $path -t $options->{ 'database' }" );
- } else {
- &Maasha::Common::run( "formatdb", "-p F -i $path -t $options->{ 'database' }" );
- }
-
- unlink $path;
-}
-
-
-sub script_blast_seq
-{
- # Martin A. Hansen, September 2007.
-
- # BLASTs sequences in stream against a given database.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $genome, $q_type, $s_type, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields );
-
- $options->{ "e_val" } = 10 if not defined $options->{ "e_val" };
- $options->{ "filter" } = "F";
- $options->{ "filter" } = "T" if $options->{ "filter" };
- $options->{ "cpus" } ||= 1;
-
- $options->{ "database" } = &Maasha::Config::genome_blast( $options->{ 'genome' } ) if $options->{ 'genome' };
-
- $tmp_in = "$TMP_DIR/blast_query.seq";
- $tmp_out = "$TMP_DIR/blast.result";
-
- $fh_out = &Maasha::Common::write_open( $tmp_in );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
- {
- $q_type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $q_type;
-
- &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out );
- }
-
- &put_record( $record, $out );
- }
-
- close $fh_out;
-
- if ( -f $options->{ 'database' } . ".phr" ) {
- $s_type = "protein";
- } else {
- $s_type = "nucleotide";
- }
-
- if ( not $options->{ 'program' } )
- {
- if ( $q_type ne "protein" and $s_type ne "protein" ) {
- $options->{ 'program' } = "blastn";
- } elsif ( $q_type eq "protein" and $s_type eq "protein" ) {
- $options->{ 'program' } = "blastp";
- } elsif ( $q_type ne "protein" and $s_type eq "protein" ) {
- $options->{ 'program' } = "blastx";
- } elsif ( $q_type eq "protein" and $s_type ne "protein" ) {
- $options->{ 'program' } = "tblastn";
- }
- }
-
- &Maasha::Common::run( "blastall", "-p $options->{ 'program' } -e $options->{ 'e_val' } -a $options->{ 'cpus' } -m 8 -i $tmp_in -d $options->{ 'database' } -F $options->{ 'filter' } -o $tmp_out > /dev/null 2>&1", 1 );
-
- unlink $tmp_in;
-
- $fh_out = &Maasha::Common::read_open( $tmp_out );
-
- undef $record;
-
- while ( $line = <$fh_out> )
- {
- chomp $line;
-
- next if $line =~ /^#/;
-
- @fields = split /\s+/, $line;
-
- $record->{ "REC_TYPE" } = "BLAST";
- $record->{ "Q_ID" } = $fields[ 0 ];
- $record->{ "S_ID" } = $fields[ 1 ];
- $record->{ "IDENT" } = $fields[ 2 ];
- $record->{ "ALIGN_LEN" } = $fields[ 3 ];
- $record->{ "MISMATCHES" } = $fields[ 4 ];
- $record->{ "GAPS" } = $fields[ 5 ];
- $record->{ "Q_BEG" } = $fields[ 6 ] - 1; # BLAST is 1-based
- $record->{ "Q_END" } = $fields[ 7 ] - 1; # BLAST is 1-based
- $record->{ "S_BEG" } = $fields[ 8 ] - 1; # BLAST is 1-based
- $record->{ "S_END" } = $fields[ 9 ] - 1; # BLAST is 1-based
- $record->{ "E_VAL" } = $fields[ 10 ];
- $record->{ "BIT_SCORE" } = $fields[ 11 ];
-
- if ( $record->{ "S_BEG" } > $record->{ "S_END" } )
- {
- $record->{ "STRAND" } = '-';
-
- ( $record->{ "S_BEG" }, $record->{ "S_END" } ) = ( $record->{ "S_END" }, $record->{ "S_BEG" } );
- }
- else
- {
- $record->{ "STRAND" } = '+';
- }
-
- &put_record( $record, $out );
- }
-
- close $fh_out;
-
- unlink $tmp_out;
-}
-
-
-sub script_blat_seq
-{
- # Martin A. Hansen, August 2007.
-
- # BLATs sequences in stream against a given genome.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $blat_args, $genome_file, $query_file, $fh_in, $fh_out, $type, $record, $result_file, $entries );
-
- $genome_file = &Maasha::Config::genome_fasta( $options->{ "genome" } );
-
- $options->{ 'tile_size' } ||= 11;
- $options->{ 'one_off' } ||= 0;
- $options->{ 'min_identity' } ||= 90;
- $options->{ 'min_score' } ||= 0;
- $options->{ 'step_size' } ||= $options->{ 'tile_size' };
-
- $blat_args .= " -tileSize=$options->{ 'tile_size' }";
- $blat_args .= " -oneOff=$options->{ 'one_off' }";
- $blat_args .= " -minIdentity=$options->{ 'min_identity' }";
- $blat_args .= " -minScore=$options->{ 'min_score' }";
- $blat_args .= " -stepSize=$options->{ 'step_size' }";
- $blat_args .= " -ooc=" . &Maasha::Config::genome_blat_ooc( $options->{ "genome" }, 11 ) if $options->{ 'ooc' };
-
- $query_file = "$TMP_DIR/blat.seq";
-
- $fh_out = &Maasha::Common::write_open( $query_file );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
- {
- &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_out, 80 );
- $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
- }
-
- &put_record( $record, $out );
- }
-
- close $fh_out;
-
- $blat_args .= " -t=dnax" if $type eq "protein";
- $blat_args .= " -q=$type";
-
- $result_file = "$TMP_DIR/blat.psl";
-
- &Maasha::Common::run( "blat", "$genome_file $query_file $blat_args $result_file > /dev/null 2>&1" );
-
- unlink $query_file;
-
- $entries = &Maasha::UCSC::psl_get_entries( $result_file );
-
- map { &put_record( $_, $out ) } @{ $entries };
-
- unlink $result_file;
-}
-
-
-sub script_match_seq
-{
- # Martin A. Hansen, August 2007.
-
- # BLATs sequences in stream against a given genome.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, @entries, $results );
-
- $options->{ "word_size" } ||= 20;
- $options->{ "direction" } ||= "both";
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
- push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
- }
-
- &put_record( $record, $out );
- }
-
- if ( @entries == 1 )
- {
- $results = &Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 0 ] ], $options, $TMP_DIR );
-
- map { &put_record( $_, $out ) } @{ $results };
- }
- elsif ( @entries == 2 )
- {
- $results = &Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 1 ] ], $options, $TMP_DIR );
-
- map { &put_record( $_, $out ) } @{ $results };
- }
-}
-
-
-sub script_create_vmatch_index
-{
- # Martin A. Hansen, January 2008.
-
- # Create a vmatch index from sequences in the stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file_tmp, $fh_tmp, $type );
-
- if ( $options->{ "index_name" } )
- {
- $file_tmp = $options->{ 'index_name' };
- $fh_tmp = &Maasha::Common::write_open( $file_tmp );
- }
-
- while ( $record = &get_record( $in ) )
- {
- if ( $options->{ "index_name" } and $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
- {
- &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_tmp );
-
- $type = &Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- if ( $options->{ "index_name" } )
- {
- close $fh_tmp;
-
- if ( $type eq "protein" ) {
- &Maasha::Common::run( "mkvtree", "-db $file_tmp -protein -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
- } else {
- &Maasha::Common::run( "mkvtree", "-db $file_tmp -dna -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
- }
-
- unlink $file_tmp;
- }
-}
-
-
-sub script_vmatch_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Vmatches sequences in stream against a given genome.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( @index_files, @records, $result_file, $fh_in, $record );
-
- $options->{ 'count' } = 1 if $options->{ 'max_hits' };
-
- if ( $options->{ "index_name" } ) {
- @index_files = $options->{ "index_name" };
- } else {
- @index_files = &Maasha::Config::genome_vmatch( $options->{ "genome" } );
- }
-
- while ( $record = &get_record( $in ) )
- {
- push @records, $record;
-
- &put_record( $record, $out );
- }
-
- $result_file = &Maasha::Match::match_vmatch( $TMP_DIR, \@records, \@index_files, $options );
-
- undef @records;
-
- $fh_in = &Maasha::Common::read_open( $result_file );
-
- while ( $record = &Maasha::Match::vmatch_get_entry( $fh_in ) ) {
- &put_record( $record, $out );
- }
-
- close $fh_in;
-
- unlink $result_file;
-}
-
-
-sub script_write_fasta
-{
- # Martin A. Hansen, August 2007.
-
- # Write FASTA entries from sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $fh );
-
- $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
- &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh, $options->{ "wrap" } );
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- close $fh;
-}
-
-
-sub script_write_align
-{
- # Martin A. Hansen, August 2007.
-
- # Write pretty alignments aligned sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $fh, $record, $align, $old_align, @entries );
-
- $fh = &write_stream( $options->{ "data_out" } ) ;
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "ALIGN" } and $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
- {
- $align = $record->{ "ALIGN" };
-
- if ( not $old_align )
- {
- push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
-
- $old_align = $align;
- }
- elsif ( $align == $old_align )
- {
- push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
- }
- else
- {
- if ( scalar( @entries ) == 2 ) {
- &Maasha::Align::align_print_pairwise( $entries[ 0 ], $entries[ 1 ], $fh, $options->{ "wrap" } );
- } elsif ( scalar ( @entries ) > 2 ) {
- &Maasha::Align::align_print_multi( \@entries, $fh, $options->{ "wrap" }, $options->{ "no_ruler" }, $options->{ "no_consensus" } );
- }
-
- undef @entries;
- $old_align = $align;
- }
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- if ( scalar( @entries ) == 2 ) {
- &Maasha::Align::align_print_pairwise( $entries[ 0 ], $entries[ 1 ], $fh, $options->{ "wrap" } );
- } elsif ( scalar ( @entries ) > 2 ) {
- &Maasha::Align::align_print_multi( \@entries, $fh, $options->{ "wrap" }, $options->{ "no_ruler" }, $options->{ "no_consensus" } );
- }
-
- close $fh if $fh;
-}
-
-
-sub script_write_blast
-{
- # Martin A. Hansen, November 2007.
-
- # Write data in blast table format (-m8 and 9).
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $fh, $record, $first );
-
- $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } ) ;
-
- $first = 1;
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "REC_TYPE" } eq "BLAST" )
- {
- if ( $options->{ "comment" } and $first )
- {
- print "# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score\n";
-
- $first = 0;
- }
-
- if ( $record->{ "STRAND" } eq "-" ) {
- ( $record->{ "S_BEG" }, $record->{ "S_END" } ) = ( $record->{ "S_END" }, $record->{ "S_BEG" } );
- }
-
- print $fh join( "\t",
- $record->{ "Q_ID" },
- $record->{ "S_ID" },
- $record->{ "IDENT" },
- $record->{ "ALIGN_LEN" },
- $record->{ "MISMATCHES" },
- $record->{ "GAPS" },
- $record->{ "Q_BEG" } + 1,
- $record->{ "Q_END" } + 1,
- $record->{ "S_BEG" } + 1,
- $record->{ "S_END" } + 1,
- $record->{ "E_VAL" },
- $record->{ "BIT_SCORE" }
- ), "\n";
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- close $fh;
-}
-
-
-sub script_write_tab
-{
- # Martin A. Hansen, August 2007.
-
- # Write data as table.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $fh, $record, $key, @keys, @vals, $ok, %no_keys, $A, $B );
-
- $options->{ "delimit" } ||= "\t";
-
- map { $no_keys{ $_ } = 1 } @{ $options->{ "no_keys" } };
-
- $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = &get_record( $in ) )
- {
- undef @vals;
- $ok = 1;
-
- if ( $options->{ "keys" } )
- {
- map { $ok = 0 if not exists $record->{ $_ } } @{ $options->{ "keys" } };
-
- if ( $ok )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( exists $record->{ $key } )
- {
- push @keys, $key if $options->{ "comment" };
- push @vals, $record->{ $key };
- }
- }
- }
- }
- else
- {
- foreach $key ( sort { $A = $a; $B = $b; $A =~ s/^V(\d+)$/$1/; $B =~ s/^V(\d+)$/$1/; $A <=> $B } keys %{ $record } )
- {
- next if exists $no_keys{ $key };
-
- push @keys, $key if $options->{ "comment" };
- push @vals, $record->{ $key };
- }
- }
-
- if ( @keys and $options->{ "comment" } )
- {
- print $fh "#", join( $options->{ "delimit" }, @keys ), "\n";
-
- delete $options->{ "comment" };
- }
-
- print $fh join( $options->{ "delimit" }, @vals ), "\n" if @vals;
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- close $fh;
-}
-
-
-sub script_write_bed
-{
- # Martin A. Hansen, August 2007.
-
- # Write BED format for the UCSC genome browser using records in stream.
-
- # Crude - needs lots of work!
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $fh, $record, $new_record );
-
- $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "REC_TYPE" } eq "BED" ) # ---- Hits from BED ----
- {
- &Maasha::UCSC::bed_put_entry( $record, $fh, $record->{ "BED_COLS" } );
- }
- elsif ( $record->{ "REC_TYPE" } eq "PSL" and $record->{ "S_ID" } =~ /^chr/i ) # ---- Hits from BLAT (PSL) ----
- {
- $new_record->{ "CHR" } = $record->{ "S_ID" };
- $new_record->{ "CHR_BEG" } = $record->{ "S_BEG" };
- $new_record->{ "CHR_END" } = $record->{ "S_END" };
- $new_record->{ "Q_ID" } = $record->{ "Q_ID" };
- $new_record->{ "SCORE" } = $record->{ "SCORE" } || 999;
- $new_record->{ "STRAND" } = $record->{ "STRAND" };
-
- &Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
- }
- elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } ) # ---- Hits from patscan_seq ----
- {
- &Maasha::UCSC::bed_put_entry( $record, $fh, 6 );
- }
- elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/i ) # ---- Hits from BLAST ----
- {
- $new_record->{ "CHR" } = $record->{ "S_ID" };
- $new_record->{ "CHR_BEG" } = $record->{ "S_BEG" };
- $new_record->{ "CHR_END" } = $record->{ "S_END" };
- $new_record->{ "Q_ID" } = $record->{ "Q_ID" };
- $new_record->{ "SCORE" } = $record->{ "SCORE" } || 999; # or use E_VAL somehow
- $new_record->{ "STRAND" } = $record->{ "STRAND" };
-
- &Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
- }
- elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and $record->{ "S_ID" } =~ /^chr/i ) # ---- Hits from Vmatch ----
- {
- $new_record->{ "CHR" } = $record->{ "S_ID" };
- $new_record->{ "CHR_BEG" } = $record->{ "S_BEG" };
- $new_record->{ "CHR_END" } = $record->{ "S_END" };
- $new_record->{ "Q_ID" } = $record->{ "Q_ID" };
- $new_record->{ "SCORE" } = $record->{ "SCORE" } || 999; # or use E_VAL somehow
- $new_record->{ "STRAND" } = $record->{ "STRAND" };
-
- &Maasha::UCSC::bed_put_entry( $new_record, $fh, 6 );
- }
- elsif ( $record->{ "CHR" } and defined $record->{ "CHR_BEG" } and $record->{ "CHR_END" } ) # ---- Generic data from tables ----
- {
- &Maasha::UCSC::bed_put_entry( $record, $fh );
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- close $fh;
-}
-
-
-sub script_write_psl
-{
- # Martin A. Hansen, August 2007.
-
- # Write PSL output from stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $fh, $record, @output, $first );
-
- $first = 1;
-
- $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = &get_record( $in ) )
- {
- &put_record( $record, $out ) if not $options->{ "no_stream" };
-
- if ( $record->{ "REC_TYPE" } and $record->{ "REC_TYPE" } eq "PSL" )
- {
- &Maasha::UCSC::psl_put_header( $fh ) if $first;
- &Maasha::UCSC::psl_put_entry( $record, $fh );
- $first = 0;
- }
- }
-
- close $fh;
-}
-
-
-sub script_write_2bit
-{
- # Martin A. Hansen, March 2008.
-
- # Write sequence entries from stream in 2bit format.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $mask, $tmp_file, $fh_tmp, $fh_in, $fh_out );
-
- $mask = 1 if not $options->{ "no_mask" };
-
- $tmp_file = "$TMP_DIR/write_2bit.fna";
- $fh_tmp = &Maasha::Common::write_open( $tmp_file );
-
- $fh_out = &write_stream( $options->{ "data_out" } );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
- &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ], $fh_tmp );
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- close $fh_tmp;
-
- $fh_in = &Maasha::Common::read_open( $tmp_file );
-
- &Maasha::TwoBit::fasta2twobit( $fh_in, $fh_out, $mask );
-
- close $fh_in;
- close $fh_out;
-
- unlink $tmp_file;
-}
-
-
-sub script_write_solid
-{
- # Martin A. Hansen, April 2008.
-
- # Write di-base encoded Solid sequence from entries in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $fh, $seq_cs );
-
- $fh = &write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } )
- {
- $seq_cs = &Maasha::Solid::seq2color_space( $record->{ "SEQ" } );
-
- &Maasha::Fasta::put_entry( [ $record->{ "SEQ_NAME" }, $seq_cs ], $fh, $options->{ "wrap" } );
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- close $fh;
-}
-
-
-sub script_plot_seqlogo
-{
- # Martin A. Hansen, August 2007.
-
- # Calculates and writes a sequence logo for alignments.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, @entries, $logo, $fh );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
- push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $logo = &Maasha::Plot::seq_logo( \@entries );
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- print $fh $logo;
-
- close $fh;
-}
-
-
-sub script_plot_phastcons_profiles
-{
- # Martin A. Hansen, January 2008.
-
- # Plots PhastCons profiles.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $phastcons_file, $phastcons_index, $index, $fh_phastcons, $record, $scores, $AoA, $plot, $fh );
-
- $options->{ "title" } ||= "PhastCons Profiles";
-
- $phastcons_file = &Maasha::Config::genome_phastcons( $options->{ "genome" } );
- $phastcons_index = &Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
-
- $index = &Maasha::UCSC::phastcons_index_retrieve( $phastcons_index );
- $fh_phastcons = &Maasha::Common::read_open( $phastcons_file );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
- {
- $scores = &Maasha::UCSC::phastcons_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } );
-
- push @{ $AoA }, [ @{ $scores } ];
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- &Maasha::UCSC::phastcons_normalize( $AoA );
-
- $AoA = [ [ &Maasha::UCSC::phastcons_mean( $AoA ) ] ] if $options->{ "mean" };
- $AoA = [ [ &Maasha::UCSC::phastcons_median( $AoA ) ] ] if $options->{ "median" };
-
- $AoA = &Maasha::Matrix::matrix_flip( $AoA );
-
- $plot = &Maasha::Plot::lineplot_simple( $AoA, $options, $TMP_DIR );
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- print $fh "$_\n" foreach @{ $plot };
-
- close $fh;
-}
-
-
-sub script_analyze_bed
-{
- # Martin A. Hansen, March 2008.
-
- # Analyze BED entries in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record );
-
- while ( $record = &get_record( $in ) )
- {
- $record = &Maasha::UCSC::bed_analyze( $record ) if $record->{ "REC_TYPE" } eq "BED";
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_analyze_vals
-{
- # Martin A. Hansen, August 2007.
-
- # Analyze values for given keys in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $key, @keys, %key_hash, $analysis, $len );
-
- map { $key_hash{ $_ } = 1 } @{ $options->{ "keys" } };
-
- while ( $record = &get_record( $in ) )
- {
- foreach $key ( keys %{ $record } )
- {
- next if $options->{ "keys" } and not exists $key_hash{ $key };
-
- $analysis->{ $key }->{ "COUNT" }++;
-
- if ( &Maasha::Calc::is_a_number( $record->{ $key } ) )
- {
- $analysis->{ $key }->{ "TYPE" } = "num";
- $analysis->{ $key }->{ "SUM" } += $record->{ $key };
- $analysis->{ $key }->{ "MAX" } = $record->{ $key } if $record->{ $key } > $analysis->{ $key }->{ "MAX" } or not $analysis->{ $key }->{ "MAX" };
- $analysis->{ $key }->{ "MIN" } = $record->{ $key } if $record->{ $key } < $analysis->{ $key }->{ "MIN" } or not $analysis->{ $key }->{ "MIN" };
- }
- else
- {
- $len = length $record->{ $key };
-
- $analysis->{ $key }->{ "TYPE" } = "alph";
- $analysis->{ $key }->{ "SUM" } += $len;
- $analysis->{ $key }->{ "MAX" } = $len if $len > $analysis->{ $key }->{ "MAX" } or not $analysis->{ $key }->{ "MAX" };
- $analysis->{ $key }->{ "MIN" } = $len if $len < $analysis->{ $key }->{ "MIM" } or not $analysis->{ $key }->{ "MIN" };
- }
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- foreach $key ( keys %{ $analysis } )
- {
- $analysis->{ $key }->{ "MEAN" } = sprintf "%.2f", $analysis->{ $key }->{ "SUM" } / $analysis->{ $key }->{ "COUNT" };
- $analysis->{ $key }->{ "SUM" } = sprintf "%.2f", $analysis->{ $key }->{ "SUN" };
- }
-
- my ( $keys, $types, $counts, $mins, $maxs, $sums, $means );
-
- $keys = "KEY ";
- $types = "TYPE ";
- $counts = "COUNT";
- $mins = "MIN ";
- $maxs = "MAX ";
- $sums = "SUM ";
- $means = "MEAN ";
-
- if ( $options->{ "keys" } ) {
- @keys = @{ $options->{ "keys" } };
- } else {
- @keys = keys %{ $analysis };
- }
-
- foreach $key ( @keys )
- {
- $keys .= sprintf "% 15s", $key;
- $types .= sprintf "% 15s", $analysis->{ $key }->{ "TYPE" };
- $counts .= sprintf "% 15s", $analysis->{ $key }->{ "COUNT" };
- $mins .= sprintf "% 15s", $analysis->{ $key }->{ "MIN" };
- $maxs .= sprintf "% 15s", $analysis->{ $key }->{ "MAX" };
- $sums .= sprintf "% 15s", $analysis->{ $key }->{ "SUM" };
- $means .= sprintf "% 15s", $analysis->{ $key }->{ "MEAN" };
- }
-
- print $out "$keys\n";
- print $out "$types\n";
- print $out "$counts\n";
- print $out "$mins\n";
- print $out "$maxs\n";
- print $out "$sums\n";
- print $out "$means\n";
-}
-
-
-sub script_head_records
-{
- # Martin A. Hansen, August 2007.
-
- # Display the first sequences in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $count );
-
- $options->{ "num" } ||= 10;
-
- $count = 0;
-
- while ( $record = &get_record( $in ) )
- {
- $count++;
-
- &put_record( $record, $out );
-
- last if $count == $options->{ "num" };
- }
-}
-
-
-sub script_remove_keys
-{
- # Martin A. Hansen, August 2007.
-
- # Remove keys from stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $new_record );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $options->{ "keys" } )
- {
- map { delete $record->{ $_ } } @{ $options->{ "keys" } };
- }
- elsif ( $options->{ "save_keys" } )
- {
- map { $new_record->{ $_ } = $record->{ $_ } if exists $record->{ $_ } } @{ $options->{ "save_keys" } };
-
- $record = $new_record;
- }
-
- &put_record( $record, $out ) if keys %{ $record };
- }
-}
-
-
-sub script_rename_keys
-{
- # Martin A. Hansen, August 2007.
-
- # Rename keys in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record );
-
- while ( $record = &get_record( $in ) )
- {
- if ( exists $record->{ $options->{ "keys" }->[ 0 ] } )
- {
- $record->{ $options->{ "keys" }->[ 1 ] } = $record->{ $options->{ "keys" }->[ 0 ] };
-
- delete $record->{ $options->{ "keys" }->[ 0 ] };
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_uniq_vals
-{
- # Martin A. Hansen, August 2007.
-
- # Find unique values in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( %hash, $record );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ $options->{ "key" } } )
- {
- if ( not $hash{ $record->{ $options->{ "key" } } } and not $options->{ "invert" } )
- {
- &put_record( $record, $out );
-
- $hash{ $record->{ $options->{ "key" } } } = 1;
- }
- elsif ( $hash{ $record->{ $options->{ "key" } } } and $options->{ "invert" } )
- {
- &put_record( $record, $out );
- }
- else
- {
- $hash{ $record->{ $options->{ "key" } } } = 1;
- }
- }
- else
- {
- &put_record( $record, $out );
- }
- }
-}
-
-
-sub script_merge_vals
-{
- # Martin A. Hansen, August 2007.
-
- # Rename keys in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, @join, $i );
-
- $options->{ "delimit" } ||= '_';
-
- while ( $record = &get_record( $in ) )
- {
- if ( exists $record->{ $options->{ "keys" }->[ 0 ] } )
- {
- @join = $record->{ $options->{ "keys" }->[ 0 ] };
-
- for ( $i = 1; $i < @{ $options->{ "keys" } }; $i++ ) {
- push @join, $record->{ $options->{ "keys" }->[ $i ] } if exists $record->{ $options->{ "keys" }->[ $i ] };
- }
-
- $record->{ $options->{ "keys" }->[ 0 ] } = join $options->{ "delimit" }, @join;
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_grab
-{
- # Martin A. Hansen, August 2007.
-
- # Grab for records in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $patterns, $pattern, $record, $key, $pos, $op, $val, %lookup_hash );
-
- if ( $options->{ "patterns" } )
- {
- $patterns = [ split ",", $options->{ "patterns" } ];
- }
- elsif ( -f $options->{ "patterns_in" } )
- {
- $patterns = &Maasha::Patscan::read_patterns( $options->{ "patterns_in" } );
- }
- elsif ( -f $options->{ "exact_in" } )
- {
- $patterns = &Maasha::Patscan::read_patterns( $options->{ "exact_in" } );
-
- map { $lookup_hash{ $_ } = 1 } @{ $patterns };
-
- undef $patterns;
- }
-
- if ( $options->{ "eval" } )
- {
- if ( $options->{ "eval" } =~ /^([^><=! ]+)\s*(>=|<=|>|<|=|!=|eq|ne)\s*(.+)$/ )
- {
- $key = $1;
- $op = $2;
- $val = $3;
- }
- }
-
- while ( $record = &get_record( $in ) )
- {
- $pos = -1;
-
- if ( %lookup_hash )
- {
- if ( $options->{ "keys" } )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( exists $lookup_hash{ $record->{ $key } } )
- {
- $pos = 1;
- goto FOUND;
- }
- }
- }
- else
- {
- foreach $key ( keys %{ $record } )
- {
- if ( not $options->{ "vals_only" } )
- {
- if ( exists $lookup_hash{ $key } )
- {
- $pos = 1;
- goto FOUND;
- }
- }
-
- if ( not $options->{ "keys_only" } )
- {
- if ( exists $lookup_hash{ $record->{ $key } } )
- {
- $pos = 1;
- goto FOUND;
- }
- }
- }
- }
- }
- elsif ( $patterns )
- {
- foreach $pattern ( @{ $patterns } )
- {
- if ( $options->{ "keys" } )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- $pos = index $record->{ $key }, $pattern;
-
- goto FOUND if $pos >= 0;
- }
- }
- else
- {
- foreach $key ( keys %{ $record } )
- {
- if ( not $options->{ "vals_only" } )
- {
- $pos = index $key, $pattern;
-
- goto FOUND if $pos >= 0;
- }
-
- if ( not $options->{ "keys_only" } )
- {
- $pos = index $record->{ $key }, $pattern;
-
- goto FOUND if $pos >= 0;
- }
- }
- }
- }
- }
- elsif ( $options->{ "regex" } )
- {
- if ( $options->{ "keys" } )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $options->{ "case_insensitive" } ) {
- $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/i;
- } else {
- $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/;
- }
-
- goto FOUND if $pos >= 0;
- }
- }
- else
- {
- foreach $key ( keys %{ $record } )
- {
- if ( not $options->{ "vals_only" } )
- {
- if ( $options->{ "case_insensitive" } ) {
- $pos = 1 if $key =~ /$options->{'regex'}/i;
- } else {
- $pos = 1 if $key =~ /$options->{'regex'}/;
- }
-
- goto FOUND if $pos >= 0;
- }
-
- if ( not $options->{ "keys_only" } )
- {
- if ( $options->{ "case_insensitive" } ) {
- $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/i;
- } else {
- $pos = 1 if $record->{ $key } =~ /$options->{'regex'}/;
- }
-
- goto FOUND if $pos >= 0;
- }
- }
- }
- }
- elsif ( $options->{ "eval" } )
- {
- if ( defined $record->{ $key } )
- {
- if ( $op eq "<" and $record->{ $key } < $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq ">" and $record->{ $key } > $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq ">=" and $record->{ $key } >= $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq "<=" and $record->{ $key } <= $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq "=" and $record->{ $key } == $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq "!=" and $record->{ $key } != $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq "eq" and $record->{ $key } eq $val ) {
- $pos = 1 and goto FOUND;
- } elsif ( $op eq "ne" and $record->{ $key } ne $val ) {
- $pos = 1 and goto FOUND;
- }
- }
- }
-
- FOUND:
-
- if ( $pos >= 0 and not $options->{ "invert" } ) {
- &put_record( $record, $out );
- } elsif ( $pos < 0 and $options->{ "invert" } ) {
- &put_record( $record, $out );
- }
- }
-}
-
-
-sub script_compute
-{
- # Martin A. Hansen, August 2007.
-
- # Evaluate extression for records in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $eval_key, $eval_val, $check, @keys );
-
- while ( $record = &get_record( $in ) )
- {
- if ( $options->{ "eval" } )
- {
- if ( $options->{ "eval" } =~ /^(.+)\s*=\s*(.+)$/ )
- {
- $eval_key = $1;
- $eval_val = $2;
- }
-
- if ( not $check )
- {
- @keys = split /\W+/, $eval_val;
- @keys = grep { ! /^\d+$/ } @keys;
-
- $check = 1;
- }
-
- map { $eval_val =~ s/$_/$record->{ $_ }/g } @keys;
-
- $record->{ $eval_key } = eval "$eval_val" or &Maasha::Common::error( "eval failed -> $@" );
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_flip_tab
-{
- # Martin A. Hansen, June 2008.
-
- # Flip a table.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $key, $A, $B, @rows, @matrix, $row, $i );
-
- while ( $record = &get_record( $in ) )
- {
- undef @rows;
-
- foreach $key ( sort { $A = $a; $B = $b; $A =~ s/^V(\d+)$/$1/; $B =~ s/^V(\d+)$/$1/; $A <=> $B } keys %{ $record } )
- {
- push @rows, $record->{ $key };
-
- }
-
- push @matrix, [ @rows ];
- }
-
- undef $record;
-
- @matrix = &Maasha::Matrix::matrix_flip( \@matrix );
-
- foreach $row ( @matrix )
- {
- for ( $i = 0; $i < @{ $row }; $i++ ) {
- $record->{ "V$i" } = $row->[ $i ];
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_add_ident
-{
- # Martin A. Hansen, May 2008.
-
- # Add a unique identifier to each record in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $key, $prefix, $i );
-
- $key = $options->{ "key" } || "ID";
- $prefix = $options->{ "prefix" } || "ID";
-
- $i = 0;
-
- while ( $record = &get_record( $in ) )
- {
- $record->{ $key } = sprintf( "$prefix%08d", $i );
-
- &put_record( $record, $out );
-
- $i++;
- }
-}
-
-
-sub script_count_records
-{
- # Martin A. Hansen, August 2007.
-
- # Count records in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $count, $result, $fh, $line );
-
- $count = 0;
-
- if ( $options->{ "no_stream" } )
- {
- while ( $line = <$in> )
- {
- chomp $line;
-
- $count++ if $line eq "---";
- }
- }
- else
- {
- while ( $record = &get_record( $in ) )
- {
- &put_record( $record, $out );
-
- $count++;
- }
- }
-
- $result = { "count_records" => $count };
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- &put_record( $result, $fh );
-
- close $fh;
-}
-
-
-sub script_random_records
-{
- # Martin A. Hansen, August 2007.
-
- # Pick a number or random records from stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $tmp_file, $fh_out, $fh_in, $count, $i, %rand_hash, $rand, $max );
-
- $options->{ "num" } ||= 10;
-
- $tmp_file = "$TMP_DIR/random_records.tmp";
-
- $fh_out = &Maasha::Common::write_open( $tmp_file );
-
- $count = 0;
-
- while ( $record = &get_record( $in ) )
- {
- &put_record( $record, $fh_out );
-
- $count++;
- }
-
- close $fh_out;
-
- $max = 0;
- $i = 0;
-
- &Maasha::Common::error( qq(Requested random records > records in stream) ) if $options->{ "num" } > $count;
-
- while ( $i < $options->{ "num" } )
- {
- $rand = int( rand( $count ) );
-
- if ( not exists $rand_hash{ $rand } )
- {
- $rand_hash{ $rand } = 1;
-
- $max = $rand if $rand > $max;
-
- $i++;
- }
- }
-
- $fh_in = &Maasha::Common::read_open( $tmp_file );
-
- $count = 0;
-
- while ( $record = &get_record( $fh_in ) )
- {
- &put_record( $record, $out ) if exists $rand_hash{ $count };
-
- last if $count == $max;
-
- $count++;
- }
-
- close $fh_in;
-
- unlink $tmp_file;
-}
-
-
-sub script_sort_records
-{
- # Martin A. Hansen, August 2007.
-
- # Sort to sort records according to keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( @keys, $key, @sort_cmd, $sort_str, $sort_sub, @records, $record, $i );
-
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $key =~ s/n$// ) {
- push @sort_cmd, qq(\$a->{ "$key" } <=> \$b->{ "$key" });
- } else {
- push @sort_cmd, qq(\$a->{ "$key" } cmp \$b->{ "$key" });
- }
- }
-
- $sort_str = join " or ", @sort_cmd;
- $sort_sub = eval "sub { $sort_str }"; # NB security issue!
-
- while ( $record = &get_record( $in ) ) {
- push @records, $record;
- }
-
- @records = sort $sort_sub @records;
-
- if ( $options->{ "reverse" } )
- {
- for ( $i = scalar @records - 1; $i >= 0; $i-- ) {
- &put_record( $records[ $i ], $out );
- }
- }
- else
- {
- for ( $i = 0; $i < scalar @records; $i++ ) {
- &put_record( $records[ $i ], $out );
- }
- }
-}
-
-
-sub script_count_vals
-{
- # Martin A. Hansen, August 2007.
-
- # Count records in stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $num, $record, %count_hash, @records, $tmp_file, $fh_out, $fh_in, $cache );
-
- $tmp_file = "$TMP_DIR/count_cache.tmp";
-
- $fh_out = &Maasha::Common::write_open( $tmp_file );
-
- $num = 0;
-
- while ( $record = &get_record( $in ) )
- {
- map { $count_hash{ $_ }{ $record->{ $_ } }++ if exists $record->{ $_ } } @{ $options->{ "keys" } };
-
- push @records, $record;
-
- if ( scalar @records > 5_000_000 ) # too many records to hold in memory - use disk cache
- {
- map { &put_record( $_, $fh_out ) } @records;
-
- undef @records;
-
- $cache = 1;
- }
-
- print STDERR "verbose: records read $num\n" if ( $options->{ 'verbose' } and ( $num % 1_000_000 ) == 0 );
-
- $num++;
- }
-
- close $fh_out;
-
- if ( $cache )
- {
- $num = 0;
-
- $fh_in = &Maasha::Common::read_open( $tmp_file );
-
- while ( $record = &get_record( $fh_in ) )
- {
- map { $record->{ $_ . "_COUNT" } = $count_hash{ $_ }{ $record->{ $_ } } if exists $record->{ $_ } } @{ $options->{ "keys" } };
-
- &put_record( $record, $out );
-
- print STDERR "verbose: cache read $num\n" if ( $options->{ 'verbose' } and ( $num % 1_000_000 ) == 0 );
-
- $num++;
- }
-
- close $fh_in;
- }
-
- foreach $record ( @records )
- {
- map { $record->{ $_ . "_COUNT" } = $count_hash{ $_ }{ $record->{ $_ } } if exists $record->{ $_ } } @{ $options->{ "keys" } };
-
- &put_record( $record, $out );
- }
-
- unlink $tmp_file;
-}
-
-
-sub script_plot_histogram
-{
- # Martin A. Hansen, September 2007.
-
- # Plot a simple histogram for a given key using GNU plot.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, %data_hash, $max, @data_list, $i, $result, $fh );
-
- $options->{ "title" } ||= "Histogram";
- $options->{ "sort" } ||= "num";
-
- while ( $record = &get_record( $in ) )
- {
- $data_hash{ $record->{ $options->{ "key" } } }++ if $record->{ $options->{ "key" } };
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- if ( $options->{ "sort" } eq "num" ) {
- map { push @data_list, [ $_, $data_hash{ $_ } ] } sort { $a <=> $b } keys %data_hash;
- } else {
- map { push @data_list, [ $_, $data_hash{ $_ } ] } sort keys %data_hash;
- }
-
- $result = &Maasha::Plot::histogram_simple( \@data_list, $options );
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- print $fh "$_\n" foreach @{ $result };
-
- close $fh;
-}
-
-
-sub script_plot_lendist
-{
- # Martin A. Hansen, August 2007.
-
- # Plot length distribution using GNU plot.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, %data_hash, $max, @data_list, $i, $result, $fh );
-
- $options->{ "title" } ||= "Length Distribution";
-
- while ( $record = &get_record( $in ) )
- {
- $data_hash{ $record->{ $options->{ "key" } } }++ if $record->{ $options->{ "key" } };
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $max = &Maasha::Calc::list_max( [ keys %data_hash ] );
-
- for ( $i = 0; $i < $max; $i++ ) {
- push @data_list, [ $i, $data_hash{ $i } || 0 ];
- }
-
- $result = &Maasha::Plot::histogram_lendist( \@data_list, $options );
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- print $fh "$_\n" foreach @{ $result };
-
- close $fh;
-}
-
-
-sub script_plot_chrdist
-{
- # Martin A. Hansen, August 2007.
-
- # Plot chromosome distribution using GNU plot.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, %data_hash, @data_list, $elem, $sort_key, $count, $result, $fh );
-
- $options->{ "title" } ||= "Chromosome Distribution";
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "CHR" } ) { # generic
- $data_hash{ $record->{ "CHR" } }++;
- } elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "S_ID" } =~ /^chr/i ) { # patscan
- $data_hash{ $record->{ "S_ID" } }++;
- } elsif ( $record->{ "REC_TYPE" } eq "PSL" and $record->{ "S_ID" } =~ /^chr/i ) { # BLAT / PSL
- $data_hash{ $record->{ "S_ID" } }++;
- } elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/i ) { # BLAST
- $data_hash{ $record->{ "S_ID" } }++;
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- foreach $elem ( keys %data_hash )
- {
- $sort_key = $elem;
-
- $sort_key =~ s/chr//i;
-
- $sort_key =~ s/^X(.*)/99$1/;
- $sort_key =~ s/^Y(.*)/99$1/;
- $sort_key =~ s/^Z(.*)/999$1/;
- $sort_key =~ s/^M(.*)/9999$1/;
- $sort_key =~ s/^U(.*)/99999$1/;
-
- $count = $sort_key =~ tr/_//;
-
- $sort_key =~ s/_.*/"999999" x $count/ex;
-
- push @data_list, [ $elem, $data_hash{ $elem }, $sort_key ];
- }
-
- @data_list = sort { $a->[ 2 ] <=> $b->[ 2 ] } @data_list;
-
- $result = &Maasha::Plot::histogram_chrdist( \@data_list, $options );
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- print $fh "$_\n" foreach @{ $result };
-
- close $fh;
-}
-
-
-sub script_plot_karyogram
-{
- # Martin A. Hansen, August 2007.
-
- # Plot hits on karyogram.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( %options, $record, @data, $fh, $result, %data_hash );
-
- $options->{ "genome" } ||= "human";
- $options->{ "feat_color" } ||= "black";
-
- while ( $record = &get_record( $in ) )
- {
- if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
- {
- push @{ $data_hash{ $record->{ "CHR" } } }, [ $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "feat_color" } ];
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $result = &Maasha::Plot::karyogram( \%data_hash, \%options );
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- print $fh $result;
-
- close $fh;
-}
-
-
-sub script_plot_matches
-{
- # Martin A. Hansen, August 2007.
-
- # Plot matches in 2D generating a dotplot.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, @data, $fh, $result, %data_hash );
-
- $options->{ "direction" } ||= "both";
-
- while ( $record = &get_record( $in ) )
- {
- if ( defined $record->{ "Q_BEG" } and defined $record->{ "S_BEG" } and $record->{ "Q_END" } and $record->{ "S_END" } ) {
- push @data, $record;
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $options->{ "title" } ||= "plot_matches";
- $options->{ "xlabel" } ||= $data[ 0 ]->{ "Q_ID" };
- $options->{ "ylabel" } ||= $data[ 0 ]->{ "S_ID" };
-
- $result = &Maasha::Plot::dotplot_matches( \@data, $options, $TMP_DIR );
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- print $fh "$_\n" foreach @{ $result };
-
- close $fh;
-}
-
-
-sub script_length_vals
-{
- # Martin A. Hansen, August 2007.
-
- # Determine the length of the value for given keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $key );
-
- while ( $record = &get_record( $in ) )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $record->{ $key } ) {
- $record->{ $key . "_LEN" } = length $record->{ $key };
- }
- }
-
- &put_record( $record, $out );
- }
-}
-
-
-sub script_sum_vals
-{
- # Martin A. Hansen, August 2007.
-
- # Calculates the sums for values of given keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $key, %sum_hash, $fh );
-
- while ( $record = &get_record( $in ) )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $record->{ $key } ) {
- $sum_hash{ $key } += $record->{ $key };
- }
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- foreach $key ( @{ $options->{ "keys" } } ) {
- &put_record( { $key . "_SUM" => $sum_hash{ $key } || 0 } , $fh );
- }
-
- close $fh;
-}
-
-
-sub script_mean_vals
-{
- # Martin A. Hansen, August 2007.
-
- # Calculate the mean of values of given keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $key, %sum_hash, %count_hash, $mean, $fh );
-
- while ( $record = &get_record( $in ) )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $record->{ $key } )
- {
- $sum_hash{ $key } += $record->{ $key };
- $count_hash{ $key }++;
- }
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $count_hash{ $key } ) {
- $mean = sprintf( "%.2f", ( $sum_hash{ $key } / $count_hash{ $key } ) );
- } else {
- $mean = "N/A";
- }
-
- &put_record( { $key . "_MEAN" => $mean } , $fh );
- }
-
- close $fh;
-}
-
-
-sub script_median_vals
-{
- # Martin A. Hansen, March 2008.
-
- # Calculate the median values of given keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $key, %median_hash, $median, $fh );
-
- while ( $record = &get_record( $in ) )
- {
- foreach $key ( @{ $options->{ "keys" } } ) {
- push @{ $median_hash{ $key } }, $record->{ $key } if defined $record->{ $key };
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $median_hash{ $key } ) {
- $median = &Maasha::Calc::median( $median_hash{ $key } );
- } else {
- $median = "N/A";
- }
-
- &put_record( { $key . "_MEDIAN" => $median } , $fh );
- }
-
- close $fh;
-}
-
-
-sub script_max_vals
-{
- # Martin A. Hansen, February 2008.
-
- # Determine the maximum values of given keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $key, $fh, %max_hash, $max_record );
-
- while ( $record = &get_record( $in ) )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $record->{ $key } )
- {
- $max_hash{ $key } = $record->{ $key } if $record->{ $key } > $max_hash{ $key };
- }
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- foreach $key ( @{ $options->{ "keys" } } )
- {
- $max_record->{ $key . "_MAX" } = $max_hash{ $key };
- }
-
- &put_record( $max_record, $fh );
-
- close $fh;
-}
-
-
-sub script_min_vals
-{
- # Martin A. Hansen, February 2008.
-
- # Determine the minimum values of given keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $key, $fh, %min_hash, $min_record );
-
- while ( $record = &get_record( $in ) )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( defined $record->{ $key } )
- {
- if ( exists $min_hash{ $key } ) {
- $min_hash{ $key } = $record->{ $key } if $record->{ $key } < $min_hash{ $key };
- } else {
- $min_hash{ $key } = $record->{ $key };
- }
- }
- }
-
- &put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $fh = &write_stream( $options->{ "data_out" } );
-
- foreach $key ( @{ $options->{ "keys" } } )
- {
- $min_record->{ $key . "_MIN" } = $min_hash{ $key };
- }
-
- &put_record( $min_record, $fh );
-
- close $fh;
-}
-
-
-sub script_upload_to_ucsc
-{
- # Martin A. Hansen, August 2007.
-
- # Calculate the mean of values of given keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, $file, $wib_file, $wig_file, $wib_dir, $fh_in, $fh_out, $i, $first, $format, $args, $type, $columns, $append, %fh_hash,
- $chr, $beg, $end, $block, $line, $max, $beg_block, $entry, $q_id, $clones );
-
- $options->{ "short_label" } ||= $options->{ 'table' };
- $options->{ "long_label" } ||= $options->{ 'table' };
- $options->{ "group" } ||= $ENV{ "LOGNAME" };
- $options->{ "priority" } ||= 1;
- $options->{ "visibility" } ||= "pack";
- $options->{ "color" } ||= join( ",", int( rand( 255 ) ), int( rand( 255 ) ), int( rand( 255 ) ) );
- $options->{ "chunk_size" } ||= 10_000_000_000; # Due to 32-bit UCSC compilation really large tables cannot be loaded in one go.
-
- $file = "$TMP_DIR/ucsc_upload.tmp";
-
- $append = 0;
-
- $first = 1;
-
- $i = 0;
-
- if ( $options->{ 'wiggle' } )
- {
- $options->{ "visibility" } = "full";
-
- while ( $record = &get_record( $in ) )
- {
- &put_record( $record, $out ) if not $options->{ "no_stream" };
-
- $record->{ "CHR" } = $record->{ "S_ID" } if not defined $record->{ "CHR" };
- $record->{ "CHR_BEG" } = $record->{ "S_BEG" } if not defined $record->{ "CHR_BEG" };
- $record->{ "CHR_END" } = $record->{ "S_END" } if not defined $record->{ "CHR_END" };
-
- $fh_hash{ $record->{ "CHR" } } = &Maasha::Common::write_open( "$TMP_DIR/$record->{ 'CHR' }" ) if not exists $fh_hash{ $record->{ "CHR" } };
-
- $fh_out = $fh_hash{ $record->{ "CHR" } };
-
- &Maasha::UCSC::bed_put_entry( $record, $fh_out, 5 );
- }
-
- map { close $_ } keys %fh_hash;
-
- $fh_out = &Maasha::Common::write_open( $file );
-
- foreach $chr ( sort keys %fh_hash )
- {
- &Maasha::Common::run( "bedSort", "$TMP_DIR/$chr $TMP_DIR/$chr" );
-
- $fh_in = &Maasha::Common::read_open( "$TMP_DIR/$chr" );
-
- undef $block;
-
- while ( $entry = &Maasha::UCSC::bed_get_entry( $fh_in, 5 ) )
- {
- $chr = $entry->{ 'CHR' };
- $beg = $entry->{ 'CHR_BEG' };
- $end = $entry->{ 'CHR_END' };
- $q_id = $entry->{ 'Q_ID' };
-
- if ( $q_id =~ /_(\d+)$/ ) {
- $clones = $1;
- } else {
- $clones = 1;
- }
-
- if ( $block )
- {
- if ( $beg > $max )
- {
- &Maasha::UCSC::fixedstep_put_entry( $chr, $beg_block, $block, $fh_out );
- undef $block;
- }
- else
- {
- for ( $i = $beg - $beg_block; $i < ( $beg - $beg_block ) + ( $end - $beg ); $i++ ) {
- $block->[ $i ] += $clones;
- }
-
- $max = &Maasha::Calc::max( $max, $end );
- }
- }
-
- if ( not $block )
- {
- $beg_block = $beg;
- $max = $end;
-
- for ( $i = 0; $i < ( $end - $beg ); $i++ ) {
- $block->[ $i ] += $clones;
- }
- }
- }
-
- close $fh_in;
-
- &Maasha::UCSC::fixedstep_put_entry( $chr, $beg_block, $block, $fh_out );
-
- unlink "$TMP_DIR/$chr";
- }
-
- close $fh_out;
-
- $wig_file = "$options->{ 'table' }.wig";
- $wib_file = "$options->{ 'table' }.wib";
-
- $wib_dir = "$ENV{ 'DATA_DIR' }/genomes/$options->{ 'database' }/wib";
-
- &Maasha::Common::dir_create_if_not_exists( $wib_dir );
-
- # &Maasha::Common::run( "wigEncode", "$file $wig_file $wib_file > /dev/null 2>&1" );
-
- `cd $TMP_DIR && wigEncode $file $wig_file $wib_file > /dev/null 2>&1`;
- &Maasha::Common::run( "mv", "$TMP_DIR/$wib_file $wib_dir" );
-
- unlink $file;
-
- $file = $wig_file;
-
- $format = "WIGGLE";
- }
- else
- {
- $fh_out = &Maasha::Common::write_open( $file );
-
- while ( $record = &get_record( $in ) )
- {
- &put_record( $record, $out ) if not $options->{ "no_stream" };
-
- if ( $record->{ "REC_TYPE" } eq "PSL" )
- {
- &Maasha::UCSC::psl_put_header( $fh_out ) if $first;
- &Maasha::UCSC::psl_put_entry( $record, $fh_out );
-
- $first = 0;
-
- $format = "PSL" if not $format;
- }
- elsif ( $record->{ "REC_TYPE" } eq "BED" and $record->{ "SEC_STRUCT" } )
- {
- # chrom chromStart chromEnd name score strand size secStr conf
-
- print $fh_out join ( "\t",
- $record->{ "CHR" },
- $record->{ "CHR_BEG" },
- $record->{ "CHR_END" } + 1,
- $record->{ "Q_ID" },
- $record->{ "SCORE" },
- $record->{ "STRAND" },
- $record->{ "SIZE" },
- $record->{ "SEC_STRUCT" },
- $record->{ "CONF" },
- ), "\n";
-
- $format = "BED_SS" if not $format;
- }
- elsif ( $record->{ "REC_TYPE" } eq "BED" )
- {
- &Maasha::UCSC::bed_put_entry( $record, $fh_out, $record->{ "BED_COLS" } );
-
- $format = "BED" if not $format;
- $columns = $record->{ "BED_COLS" } if not $columns;
- }
- elsif ( $record->{ "REC_TYPE" } eq "PATSCAN" and $record->{ "CHR" } )
- {
- &Maasha::UCSC::bed_put_entry( $record, $fh_out, 6 );
-
- $format = "BED" if not $format;
- $columns = 6 if not $columns;
- }
- elsif ( $record->{ "REC_TYPE" } eq "BLAST" and $record->{ "S_ID" } =~ /^chr/ )
- {
- $record->{ "CHR" } = $record->{ "S_ID" };
- $record->{ "CHR_BEG" } = $record->{ "S_BEG" };
- $record->{ "CHR_END" } = $record->{ "S_END" };
- $record->{ "SCORE" } = $record->{ "BIT_SCORE" } * 1000;
-
- $format = "BED" if not $format;
- $columns = 6 if not $columns;
-
- &Maasha::UCSC::bed_put_entry( $record, $fh_out );
- }
- elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and $record->{ "S_ID" } =~ /^chr/i )
- {
- $record->{ "CHR" } = $record->{ "S_ID" };
- $record->{ "CHR_BEG" } = $record->{ "S_BEG" };
- $record->{ "CHR_END" } = $record->{ "S_END" };
- $record->{ "SCORE" } = $record->{ "SCORE" } || 999;
- $record->{ "SCORE" } = int( $record->{ "SCORE" } );
-
- $format = "BED" if not $format;
- $columns = 6 if not $columns;
-
- &Maasha::UCSC::bed_put_entry( $record, $fh_out, 6 );
- }
-
- if ( $i == $options->{ "chunk_size" } )
- {
- close $fh_out;
-
- if ( $format eq "BED" ) {
- &Maasha::UCSC::bed_upload_to_ucsc( $TMP_DIR, $file, $options, $append );
- } elsif ( $format eq "PSL" ) {
- &Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
- }
-
- unlink $file;
-
- $first = 1;
-
- $append = 1;
-
- $fh_out = &Maasha::Common::write_open( $file );
- }
-
- $i++;
- }
- }
-
- close $fh_out;
-
- if ( exists $options->{ "database" } and $options->{ "table" } )
- {
- if ( $format eq "BED" )
- {
- $type = "bed $columns";
-
- &Maasha::UCSC::bed_upload_to_ucsc( $TMP_DIR, $file, $options, $append );
- }
- elsif ( $format eq "BED_SS" )
- {
- $options->{ "sec_struct" } = 1;
-
- $type = "sec_struct";
-
- &Maasha::UCSC::bed_upload_to_ucsc( $TMP_DIR, $file, $options, $append );
- }
- elsif ( $format eq "PSL" )
- {
- $type = "psl";
-
- &Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
- }
- elsif ( $format eq "WIGGLE" )
- {
- $type = "wig 0";
-
- &Maasha::UCSC::wiggle_upload_to_ucsc( $TMP_DIR, $wib_dir, $file, $options );
- }
-
- unlink $file;
-
- &Maasha::UCSC::update_my_tracks( $options, $type );
- }
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub read_stream
-{
- # Martin A. Hansen, July 2007.
-
- # Opens a stream to STDIN or a file,
-
- my ( $path, # path - OPTIONAL
- ) = @_;
-
- # Returns filehandle.
-
- my ( $fh );
-
- if ( not -t STDIN ) {
- $fh = &Maasha::Common::read_stdin();
- } elsif ( not $path ) {
-# &Maasha::Common::error( qq(no data stream) );
- } else {
- $fh = &Maasha::Common::read_open( $path );
- }
-
-# $fh->autoflush(1) if $fh;
-
- return $fh;
-}
-
-
-sub write_stream
-{
- # Martin A. Hansen, August 2007.
-
- # Opens a stream to STDOUT or a file.
-
- my ( $path, # path - OPTIONAL
- $gzip, # compress data - OPTIONAL
- ) = @_;
-
- # Returns filehandle.
-
- my ( $fh );
-
- if ( $path ) {
- $fh = &Maasha::Common::write_open( $path, $gzip );
- } else {
- $fh = &Maasha::Common::write_stdout();
- }
-
- return $fh;
-}
-
-
-sub get_record
-{
- # Martin A. Hansen, July 2007.
-
- # Reads one record at a time and converts that record
- # to a Perl data structure (a hash) which is returned.
-
- my ( $fh,
- ) = @_;
-
- # Returns data structure.
-
- my ( $block, @lines, $line, $key, $value, %record );
-
- local $/ = "\n---\n";
-
- $block = <$fh>;
-
- chomp $block;
-
- return if not defined $block;
-
- @lines = split "\n", $block;
-
- foreach $line ( @lines )
- {
- ( $key, $value ) = split ": ", $line;
-
- $record{ $key } = $value;
- }
-
- return wantarray ? %record : \%record;
-}
-
-
-sub put_record
-{
- # Martin A. Hansen, July 2007.
-
- # Given a Perl datastructure (a hash ref) emits this to STDOUT or a filehandle.
-
- my ( $data, # data structure
- $fh, # file handle - OPTIONAL
- ) = @_;
-
- # Returns nothing.
-
- if ( scalar keys %{ $data } )
- {
- if ( $fh )
- {
- map { print $fh "$_: $data->{ $_ }\n" } keys %{ $data };
- print $fh "---\n";
- }
- else
- {
- map { print "$_: $data->{ $_ }\n" } keys %{ $data };
- print "---\n";
- }
- }
-
- undef $data;
-}
-
-
-sub getopt_files
-{
- # Martin A. Hansen, November 2007.
-
- # Extracts files from an explicit GetOpt::Long argument
- # allowing for the use of glob. E.g.
- # --data_in=test.fna
- # --data_in=test.fna,test2.fna
- # --data_in=*.fna
- # --data_in=test.fna,/dir/*.fna
-
- my ( $option, # option from GetOpt::Long
- ) = @_;
-
- # Returns a list.
-
- my ( $elem, @files );
-
- foreach $elem ( split ",", $option )
- {
- if ( -f $elem ) {
- push @files, $elem;
- } elsif ( $elem =~ /\*/ ) {
- push @files, glob( $elem );
- }
- }
-
- return wantarray ? @files : \@files;
-}
-
-
-sub sig_handler
-{
- # Martin A. Hansen, April 2008.
-
- # Removes temporary directory and exits gracefully.
- # This subroutine is meant to be run always as the last
- # thing even if a script is dies or is interrupted
- # or killed.
-
- my ( $sig, # signal from the %SIG
- ) = @_;
-
- # print STDERR "signal->$sig<-\n";
-
- chomp $sig;
-
- sleep 1;
-
- if ( -d $TMP_DIR )
- {
- if ( $sig =~ /MAASHA_ERROR/ ) {
- print STDERR "\nProgram '$script' had an error" . " - Please wait for temporary data to be removed\n";
- } elsif ( $sig eq "INT" ) {
- print STDERR "\nProgram '$script' interrupted (ctrl-c was pressed)" . " - Please wait for temporary data to be removed\n";
- } elsif ( $sig eq "TERM" ) {
- print STDERR "\nProgram '$script' terminated (someone used kill?)" . " - Please wait for temporary data to be removed\n";
- } else {
- print STDERR "\nProgram '$script' died->$sig" . " - Please wait for temporary data to be removed\n";
- }
-
- # This is a really bad solution, potentially, anyone can include this module and set
- # the TMP_DIR to point at any dir and thus take out the machine !!!
-
- &Maasha::Common::dir_remove( $TMP_DIR );
- }
-
- exit( 0 );
-}
-
-
-END
-{
- # This is a really bad solution, potentially, anyone can include this module and set
- # the TMP_DIR to point at any dir and thus take out the machine !!!
-
- &Maasha::Common::dir_remove( $TMP_DIR );
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-1;
-
-__END__
-
-
-sub script_read_soft
-{
- # Martin A. Hansen, December 2007.
-
- # Read soft format.
- # http://www.ncbi.nlm.nih.gov/geo/info/soft2.html
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $data_in, $file, $num, $records, $record );
-
- while ( $record = &get_record( $in ) ) {
- &put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- $records = &Maasha::NCBI::soft_parse( $file );
-
- foreach $record ( @{ $records } )
- {
- &put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
- }
-
- NUM:
-
- close $data_in if $data_in;
-}
projects / biopieces.git / commitdiff