package Maasha::Biopieces;
-# Copyright (C) 2007-2008 Martin A. Hansen.
+# Copyright (C) 2007-2009 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
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-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::Solexa;
-use Maasha::SQL;
-use Maasha::Gwiki;
-
-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,
- SCORE => 2,
-};
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SIGNAL HANDLER <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-$SIG{ '__DIE__' } = \&sig_handler;
-$SIG{ 'INT' } = \&sig_handler;
-$SIG{ 'TERM' } = \&sig_handler;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GLOBALS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my ( $script, $BP_TMP );
-
-$script = Maasha::Common::get_scriptname();
-$BP_TMP = Maasha::Common::get_tmpdir();
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LOG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my $log_global = Maasha::Common::append_open( "$ENV{ 'BP_LOG' }/biopieces.log" );
-my $log_local = Maasha::Common::append_open( "$ENV{ 'HOME' }/.biopieces.log" );
-
-$log_global->autoflush( 1 );
-$log_local->autoflush( 1 );
-
-&log( $log_global, $script, \@ARGV );
-&log( $log_local, $script, \@ARGV );
-
-close $log_global;
-close $log_local;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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 );
-
- $options = get_options( $script );
-
- $options->{ "SCRIPT" } = $script;
-
- if ( $script ne "list_biopieces" and $script ne "list_genomes" ) {
- $script = "print_usage" if ( -t STDIN and keys %{ $options } <= 1 or $options->{ 'help' } );
- }
-
- $in = read_stream( $options->{ "stream_in" } );
- $out = write_stream( $options->{ "stream_out" } );
-
- if ( $script eq "print_usage" ) { script_print_usage( $in, $out, $options ) }
- elsif ( $script eq "list_biopieces" ) { script_list_biopieces( $in, $out, $options ) }
- elsif ( $script eq "list_genomes" ) { script_list_genomes( $in, $out, $options ) }
- elsif ( $script eq "read_fasta" ) { script_read_fasta( $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_fixedstep" ) { script_read_fixedstep( $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 "format_genome" ) { script_format_genome( $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 "soap_seq" ) { script_soap_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 ) }
- 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_fixedstep" ) { script_write_fixedstep( $in, $out, $options ) }
- elsif ( $script eq "write_2bit" ) { script_write_2bit( $in, $out, $options ) }
- elsif ( $script eq "write_solid" ) { script_write_solid( $in, $out, $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 "merge_records" ) { script_merge_records( $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;
-}
-
-
-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 "print_usage" )
- {
- @options = qw(
- data_in|i=s
- );
- }
- elsif ( $script eq "read_fasta" )
- {
- @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_fixedstep" )
- {
- @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
- samples|s=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 "format_genome" )
- {
- @options = qw(
- no_stream|x
- dir|d=s
- genome|g=s
- formats|f=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 "soap_seq" )
- {
- @options = qw(
- in_file|i=s
- genome|g=s
- seed_size|s=s
- mismatches|m=s
- gap_size|G=s
- cpus|c=s
- );
- }
- 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_fixedstep" )
- {
- @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 "merge_records" )
- {
- @options = qw(
- keys|k=s
- merge|m=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
- score|S
- log10|L
- color|c=s
- chunk_size|C=s
- );
- }
-
- push @options, qw(
- stream_in|I=s
- stream_out|O=s
- verbose
- help|?
- );
-
-# print STDERR Dumper( \@options );
-
- GetOptions(
- \%options,
- @options,
- );
-
-# print STDERR Dumper( \%options );
-
- if ( -t STDIN && scalar( keys %options ) == 0 or $options{ "help" } ) {
- return wantarray ? %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" };
- $options{ "formats" } = [ split ",", $options{ "formats" } ] if defined $options{ "formats" };
- $options{ "samples" } = [ split ",", $options{ "samples" } ] if defined $options{ "samples" };
-
- # ---- 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" and $script ne "format_genome" )
- {
- @genomes = Maasha::Common::ls_dirs( "$ENV{ 'BP_DATA' }/genomes" );
- map { $_ =~ s/.*\/(.+)$/$1/ } @genomes;
-
- if ( not grep { $_ =~ /^$options{ $opt }$/ } @genomes ) {
- Maasha::Common::error( qq(Genome $options{ $opt } not found in "$ENV{ 'BP_DATA' }/genomes/") );
- }
- }
- elsif ( $opt eq "terminal" and not $options{ $opt } =~ /^(svg|post|dumb|x11)/ )
- {
- Maasha::Common::error( qq(Bad --$opt argument "$options{ $opt }") );
- }
- elsif ( $opt eq "table" and $options{ $opt } =~ /-\./ )
- {
- Maasha::Common::error( qq(Character '$options{ $opt }' is not allowed in table names) );
- }
- elsif ( $opt eq "merge" and $options{ $opt } !~ /^(AandB|AorB|BorA|AnotB|BnotA)$/ )
- {
- Maasha::Common::error( qq(Argument to --$opt must be AandB, AorB, BorA, AnotB, or BnotA - not "$options{ $opt }") );
- }
- }
-
- 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 =~ /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_name" };
- Maasha::Common::error( qq(no --in_file or --genome specified) ) if $script eq "soap_seq" and not $options{ "genome" } and not $options{ "in_file" };
- Maasha::Common::error( qq(both --in_file and --genome specified) ) if $script eq "soap_seq" and $options{ "genome" } and $options{ "in_file" };
- Maasha::Common::error( qq(no --genome specified) ) if $script =~ /format_genome|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 ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $file, $wiki, $lines );
-
- if ( $options->{ 'data_in' } ) {
- $file = $options->{ 'data_in' };
- } else {
- $file = join "", $ENV{ 'BP_DIR' }, "/bp_usage/", $options->{ 'SCRIPT' }, ".wiki";
- }
-
- $wiki = Maasha::Gwiki::gwiki_read( $file );
-
- if ( not $options->{ "help" } ) {
- @{ $wiki } = grep { $_->[ 0 ]->{ 'SECTION' } =~ /Biopiece|Synopsis|Usage|Options|Help/ } @{ $wiki };
- }
-
- $lines = Maasha::Gwiki::gwiki2ascii( $wiki );
-
- print STDERR "$_\n" foreach @{ $lines };
-
- exit;
-}
-
-
-sub script_list_biopieces
-{
- # Martin A. Hansen, January 2008.
-
- # Prints the synopsis from the usage for each of the biopieces.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( @files, $file, $wiki, $program, $synopsis );
-
- @files = Maasha::Common::ls_files( "$ENV{ 'BP_DIR' }/bp_usage" );
-
- foreach $file ( sort @files )
- {
- if ( $file =~ /\/([a-z0-9_]+)\.wiki$/ )
- {
- $program = $1;
-
- $wiki = Maasha::Gwiki::gwiki_read( $file );
-
- @{ $wiki } = grep { $_->[ 0 ]->{ 'SECTION' } =~ /Synopsis/ } @{ $wiki };
- @{ $wiki } = grep { $_->[ 0 ]->{ 'FORMAT' } =~ /paragraph/ } @{ $wiki };
-
- $synopsis = $wiki->[ 0 ]->[ 0 ]->{ 'TEXT' };
- $synopsis =~ s/!(\w)/$1/g;
-
- printf( "%-30s%s\n", $program, $synopsis );
- }
- }
-
- exit;
-}
-
-
-sub script_list_genomes
-{
- # Martin A. Hansen, January 2008.
-
- # Prints the synopsis from the usage for each of the biopieces.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( @genomes, $genome, @formats, $format, %hash, %found, @row );
-
- @genomes = Maasha::Common::ls_dirs( "$ENV{ 'BP_DATA' }/genomes" );
-
- foreach $genome ( @genomes )
- {
- next if $genome =~ /\.$/;
-
- @formats = Maasha::Common::ls_dirs( $genome );
-
- foreach $format ( @formats )
- {
- if ( $format =~ /\/([^\/]+)\/(\w+)$/ )
- {
- $hash{ $1 }{ $2 } = 1;
-
- $found{ $2 } = 1;
- }
- }
- }
-
- @row = "Genome";
-
- map { push @row, $_ } sort keys %found;
-
- print join( "\t", @row ), "\n";
-
- foreach $genome ( sort keys %hash )
- {
- @row = $genome;
-
- foreach $format ( sort keys %found )
- {
- if ( exists $hash{ $genome }{ $format } ) {
- push @row, "yes";
- } else {
- push @row, "no";
- }
- }
-
- print join( "\t", @row ), "\n";
- }
-}
-
-
-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_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_fixedstep
-{
- # Martin A. Hansen, Juli 2008.
-
- # Read fixedStep wiggle format from stream or file.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $file, $record, $entry, $head, $chr, $chr_beg, $step, $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::fixedstep_get_entry( $data_in ) )
- {
- $head = shift @{ $entry };
-
- if ( $head =~ /^chrom=([^ ]+) start=(\d+) step=(\d+)$/ )
- {
- $record->{ "REC_TYPE" } = "fixed_step";
- $record->{ "CHR" } = $1;
- $record->{ "CHR_BEG" } = $2;
- $record->{ "STEP" } = $3;
- $record->{ "VALS" } = join ",", @{ $entry };
- }
-
- 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_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 = {
- 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::fixedstep_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, $skip );
-
- while ( $record = get_record( $in ) ) {
- put_record( $record, $out );
- }
-
- $num = 1;
-
- foreach $file ( @{ $options->{ "files" } } )
- {
- print STDERR "Creating index for file: $file\n" if $options->{ "verbose" };
-
- $soft_index = Maasha::NCBI::soft_index_file( $file );
-
- $fh = Maasha::Common::read_open( $file );
-
- @platforms = grep { $_->{ "SECTION" } =~ /PLATFORM/ } @{ $soft_index };
-
- print STDERR "Getting platform tables for file: $file\n" if $options->{ "verbose" };
-
- $plat_table = Maasha::NCBI::soft_get_platform( $fh, $platforms[ 0 ]->{ "LINE_BEG" }, $platforms[ -1 ]->{ "LINE_END" } );
-
- @samples = grep { $_->{ "SECTION" } =~ /SAMPLE/ } @{ $soft_index };
-
- $old_end = $platforms[ -1 ]->{ "LINE_END" };
-
- foreach $sample ( @samples )
- {
- $skip = 0;
- $skip = 1 if ( $options->{ "samples" } and grep { $sample->{ "SECTION" } !~ /$_/ } @{ $options->{ "samples" } } );
-
- print STDERR "Getting samples for dataset: $sample->{ 'SECTION' }\n" if $options->{ "verbose" } and not $skip;
-
- $records = Maasha::NCBI::soft_get_sample( $fh, $plat_table, $sample->{ "LINE_BEG" } - $old_end - 1, $sample->{ "LINE_END" } - $old_end - 1, $skip );
-
- foreach $record ( @{ $records } )
- {
- put_record( $record, $out );
-
- goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- $old_end = $sample->{ "LINE_END" };
- }
-
- 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, $data_in, $entry, $num, @seqs, @scores, $i );
-
- $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 );
-
- while ( $entry = Maasha::Solexa::solexa_get_entry( $data_in ) )
- {
- @seqs = split //, $entry->[ SEQ ];
- @scores = split /:/, $entry->[ SCORE ];
-
- for ( $i = 0; $i < @scores; $i++ ) {
- $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $options->{ "quality" };
- }
-
- $record->{ "SEQ_NAME" } = $entry->[ SEQ_NAME ];
- $record->{ "SEQ" } = join "", @seqs;
- $record->{ "SEQ_LEN" } = scalar @seqs;
- $record->{ "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_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_format_genome
-{
- # Martin A. Hansen, Juli 2008.
-
- # Format a genome to speficed formats.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $dir, $genome, $fasta_dir, $phastcons_dir, $vals, $fh_out, $record, $format, $index, $entry );
-
- $dir = $options->{ 'dir' } || $ENV{ 'BP_DATA' };
- $genome = $options->{ 'genome' };
-
- Maasha::Common::error( "Directory: $dir does not exist" ) if not -d $dir;
- Maasha::Common::dir_create_if_not_exists( "$dir/genomes" );
- Maasha::Common::dir_create_if_not_exists( "$dir/genomes/$genome" );
-
- if ( grep { $_ =~ /fasta|blast|vmatch/i } @{ $options->{ "formats" } } )
- {
- if ( -f "$dir/genomes/$genome/fasta/$genome.fna" )
- {
- $fasta_dir = "$dir/genomes/$genome/fasta";
- }
- else
- {
- Maasha::Common::dir_create_if_not_exists( "$dir/genomes/$genome/fasta" );
-
- $fasta_dir = "$dir/genomes/$genome/fasta";
-
- $fh_out = Maasha::Common::write_open( "$fasta_dir/$genome.fna" );
- }
- }
- elsif ( grep { $_ =~ /phastcons/i } @{ $options->{ "formats" } } )
- {
- Maasha::Common::dir_create_if_not_exists( "$dir/genomes/$genome/phastcons" );
-
- $phastcons_dir = "$dir/genomes/$genome/phastcons";
-
- $fh_out = Maasha::Common::write_open( "$phastcons_dir/$genome.pp" );
- }
-
- while ( $record = get_record( $in ) )
- {
- if ( $fh_out and $entry = record2fasta( $record ) )
- {
- Maasha::Fasta::put_entry( $entry, $fh_out, $options->{ "wrap" } );
- }
- elsif ( $fh_out and $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "STEP" } and $record->{ "VALS" } )
- {
- print $fh_out "fixedStep chrom=$record->{ 'CHR' } start=$record->{ 'CHR_BEG' } step=$record->{ 'STEP' }\n";
-
- $vals = $record->{ 'VALS' };
-
- $vals =~ tr/,/\n/;
-
- print $fh_out "$vals\n";
- }
-
- put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- foreach $format ( @{ $options->{ 'formats' } } )
- {
- if ( $format =~ /^fasta$/i ) { Maasha::Fasta::fasta_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/fasta/$genome.index" ) }
- elsif ( $format =~ /^blast$/i ) { Maasha::NCBI::blast_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/blast", "dna", $genome ) }
- elsif ( $format =~ /^blat$/i ) { print STDERR "BLAT FORMAT NOT IMPLEMENTED" }
- elsif ( $format =~ /^vmatch$/i ) { Maasha::Match::vmatch_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/vmatch", $BP_TMP ) }
- elsif ( $format =~ /^phastcons$/i ) { Maasha::UCSC::phastcons_index( "$genome.pp", $phastcons_dir ) }
- }
-
- close $fh_out if $fh_out;
-}
-
-
-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 $new_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;
- }
- }
-
- $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
-
- 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, $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 = $options->{ "genome" };
-
- $genome_file = "$ENV{ 'BP_DATA' }/genomes/$genome/fasta/$genome.fna";
- $index_file = "$ENV{ 'BP_DATA' }/genomes/$genome/fasta/$genome.index";
-
- $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( $BP_TMP, $options->{ "genome" }, $maf_track, $options->{ "chr" }, $beg, $end, $options->{ "strand" } );
-
- foreach $entry ( @{ $align } )
- {
- $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( $BP_TMP, $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( $BP_TMP, $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( $BP_TMP, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } );
- }
-
- foreach $entry ( @{ $align } )
- {
- $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->{ "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->{ "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 = {
- 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 ] }, $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" } )
- {
- 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 ] }, $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" } );
- }
-
- $genome_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna" 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' };
-
- $seq_file = "$BP_TMP/patscan.seq";
- $pat_file = "$BP_TMP/patscan.pat";
- $out_file = "$BP_TMP/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++;
- }
- }
-
- 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, $entry );
-
- $path = $options->{ "database" };
-
- $fh = Maasha::Common::write_open( $path );
-
- while ( $record = get_record( $in ) )
- {
- put_record( $record, $out ) if not $options->{ "no_stream" };
-
- if ( $entry = record2fasta( $record ) )
- {
- $seq_type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $seq_type;
-
- Maasha::Fasta::put_entry( $entry, $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, $entry );
-
- $options->{ "e_val" } = 10 if not defined $options->{ "e_val" };
- $options->{ "filter" } = "F";
- $options->{ "filter" } = "T" if $options->{ "filter" };
- $options->{ "cpus" } ||= 1;
-
- $options->{ "database" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/blast/$options->{ 'genome' }.fna" if $options->{ 'genome' };
-
- $tmp_in = "$BP_TMP/blast_query.seq";
- $tmp_out = "$BP_TMP/blast.result";
-
- $fh_out = Maasha::Common::write_open( $tmp_in );
-
- while ( $record = get_record( $in ) )
- {
- if ( $entry = record2fasta( $record ) )
- {
- $q_type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $q_type;
-
- Maasha::Fasta::put_entry( $entry, $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";
- }
- }
-
- if ( $options->{ 'verbose' } )
- {
- Maasha::Common::run(
- "blastall",
- join( " ",
- "-p $options->{ 'program' }",
- "-e $options->{ 'e_val' }",
- "-a $options->{ 'cpus' }",
- "-m 8",
- "-i $tmp_in",
- "-d $options->{ 'database' }",
- "-F $options->{ 'filter' }",
- "-o $tmp_out",
- ),
- 1
- );
- }
- else
- {
- Maasha::Common::run(
- "blastall",
- join( " ",
- "-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, $entry );
-
- $genome_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
-
- $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' };
-
- $query_file = "$BP_TMP/blat.seq";
-
- $fh_out = Maasha::Common::write_open( $query_file );
-
- while ( $record = get_record( $in ) )
- {
- if ( $entry = record2fasta( $record ) )
- {
- $type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $type;
- Maasha::Fasta::put_entry( $entry, $fh_out, 80 );
- }
-
- put_record( $record, $out );
- }
-
- close $fh_out;
-
- $blat_args .= " -t=dnax" if $type eq "protein";
- $blat_args .= " -q=$type";
-
- $result_file = "$BP_TMP/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_soap_seq
-{
- # Martin A. Hansen, July 2008.
-
- # soap sequences in stream against a given file or genome.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $genome, $tmp_in, $tmp_out, $fh_in, $fh_out, $record, $line, @fields, $entry, $count, $args );
-
- $options->{ "seed_size" } ||= 10;
- $options->{ "mismatches" } ||= 2;
- $options->{ "gap_size" } ||= 0;
- $options->{ "cpus" } ||= 1;
-
- if ( $options->{ "genome" } ) {
- $options->{ "in_file" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna";
- }
-
- $tmp_in = "$BP_TMP/soap_query.seq";
- $tmp_out = "$BP_TMP/soap.result";
-
- $fh_out = Maasha::Common::write_open( $tmp_in );
-
- $count = 0;
-
- while ( $record = get_record( $in ) )
- {
- if ( $entry = record2fasta( $record ) )
- {
- Maasha::Fasta::put_entry( $entry, $fh_out );
-
- $count++;
- }
-
- put_record( $record, $out );
- }
-
- close $fh_out;
-
- if ( $count > 0 )
- {
- $args = join( " ",
- "-s $options->{ 'seed_size' }",
- "-r 2",
- "-a $tmp_in",
- "-v $options->{ 'mismatches' }",
- "-g $options->{ 'gap_size' }",
- "-p $options->{ 'cpus' }",
- "-d $options->{ 'in_file' }",
- "-o $tmp_out",
- );
-
- $args .= " > /dev/null 2>&1" if not $options->{ 'verbose' };
-
- Maasha::Common::run( "soap", $args, 1 );
-
- unlink $tmp_in;
-
- $fh_out = Maasha::Common::read_open( $tmp_out );
-
- undef $record;
-
- while ( $line = <$fh_out> )
- {
- chomp $line;
-
- @fields = split /\t/, $line;
-
- $record->{ "REC_TYPE" } = "SOAP";
- $record->{ "Q_ID" } = $fields[ 0 ];
- $record->{ "SCORE" } = $fields[ 3 ];
- $record->{ "STRAND" } = $fields[ 6 ];
- $record->{ "S_ID" } = $fields[ 7 ];
- $record->{ "S_BEG" } = $fields[ 8 ] - 1; # soap is 1-based
- $record->{ "S_END" } = $fields[ 8 ] + $fields[ 5 ] - 2;
-
- put_record( $record, $out );
- }
-
- close $fh_out;
- }
-
- unlink $tmp_out;
-}
-
-
-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, $BP_TMP );
-
- map { put_record( $_, $out ) } @{ $results };
- }
- elsif ( @entries == 2 )
- {
- $results = Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 1 ] ], $options, $BP_TMP );
-
- 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, $entry );
-
- 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 $entry = record2fasta( $record ) )
- {
- Maasha::Fasta::put_entry( $entry, $fh_tmp );
-
- $type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not defined $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, %hash );
-
- $options->{ 'count' } = 1 if $options->{ 'max_hits' };
-
- if ( $options->{ "index_name" } )
- {
- @index_files = $options->{ "index_name" };
- }
- else
- {
- @index_files = Maasha::Common::ls_files( "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/vmatch" );
-
- map { $_ =~ /^(.+)\.[a-z1]{3,4}$/; $hash{ $1 } = 1 } @index_files;
-
- @index_files = sort keys %hash;
- }
-
- while ( $record = get_record( $in ) )
- {
- push @records, $record;
-
- put_record( $record, $out );
- }
-
- $result_file = Maasha::Match::match_vmatch( $BP_TMP, \@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, $entry );
-
- $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = get_record( $in ) )
- {
- if ( $entry = record2fasta( $record ) ) {
- Maasha::Fasta::put_entry( $entry, $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, @entries );
-
- $fh = write_stream( $options->{ "data_out" } ) ;
-
- 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" };
- }
-
- 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.
-
- 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->{ "REC_TYPE" } eq "SOAP" 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;
- $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_fixedstep
-{
- # Martin A. Hansen, Juli 2008.
-
- # Write fixedStep entries from recrods in the stream.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $fh, $record, $vals );
-
- $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = get_record( $in ) )
- {
- if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "STEP" } and $record->{ "VALS" } )
- {
- print $fh "fixedStep chrom=$record->{ 'CHR' } start=$record->{ 'CHR_BEG' } step=$record->{ 'STEP' }\n";
-
- $vals = $record->{ 'VALS' };
-
- $vals =~ tr/,/\n/;
-
- print $fh "$vals\n";
- }
-
- put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- 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, $entry );
-
- $mask = 1 if not $options->{ "no_mask" };
-
- $tmp_file = "$BP_TMP/write_2bit.fna";
- $fh_tmp = Maasha::Common::write_open( $tmp_file );
-
- $fh_out = write_stream( $options->{ "data_out" } );
-
- while ( $record = get_record( $in ) )
- {
- if ( $entry = record2fasta( $record ) ) {
- Maasha::Fasta::put_entry( $entry, $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, $entry );
-
- $fh = write_stream( $options->{ "data_out" }, $options->{ "compress" } );
-
- while ( $record = get_record( $in ) )
- {
- if ( $entry = record2fasta( $record ) )
- {
- $entry->[ SEQ ] = Maasha::Solid::seq2color_space( uc $entry->[ SEQ ] );
-
- Maasha::Fasta::put_entry( $entry, $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, $BP_TMP );
-
- $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 }->{ "SUM" };
- }
-
- 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_merge_records
-{
- # Martin A. Hansen, July 2008.
-
- # Merges records in the stream based on identical values of two given keys.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $merge, $record, $file1, $file2, $fh1, $fh2, $key1, $key2, @keys1, @keys2, @vals1, @vals2,
- $num1, $num2, $num, $cmp, $i );
-
- $merge = $options->{ "merge" } || "AandB";
-
- $file1 = "$BP_TMP/merge_records1.tmp";
- $file2 = "$BP_TMP/merge_records2.tmp";
-
- $fh1 = Maasha::Common::write_open( $file1 );
- $fh2 = Maasha::Common::write_open( $file2 );
-
- $key1 = $options->{ "keys" }->[ 0 ];
- $key2 = $options->{ "keys" }->[ 1 ];
-
- $num = $key2 =~ s/n$//;
- $num1 = 0;
- $num2 = 0;
-
- while ( $record = get_record( $in ) )
- {
- if ( exists $record->{ $key1 } )
- {
- @keys1 = $key1;
- @vals1 = $record->{ $key1 };
-
- delete $record->{ $key1 };
-
- map { push @keys1, $_; push @vals1, $record->{ $_ } } keys %{ $record };
-
- print $fh1 join( "\t", @vals1 ), "\n";
-
- $num1++;
- }
- elsif ( exists $record->{ $key2 } )
- {
- @keys2 = $key2;
- @vals2 = $record->{ $key2 };
-
- delete $record->{ $key2 };
-
- map { push @keys2, $_; push @vals2, $record->{ $_ } } keys %{ $record };
-
- print $fh2 join( "\t", @vals2 ), "\n";
-
- $num2++;
- }
- }
-
- close $fh1;
- close $fh2;
-
- if ( $num )
- {
- Maasha::Common::run( "sort", "-k 1,1n $file1 > $file1.sort" ) and rename "$file1.sort", $file1;
- Maasha::Common::run( "sort", "-k 1,1n $file2 > $file2.sort" ) and rename "$file2.sort", $file2;
- }
- else
- {
- Maasha::Common::run( "sort", "-k 1,1 $file1 > $file1.sort" ) and rename "$file1.sort", $file1;
- Maasha::Common::run( "sort", "-k 1,1 $file2 > $file2.sort" ) and rename "$file2.sort", $file2;
- }
-
- $fh1 = Maasha::Common::read_open( $file1 );
- $fh2 = Maasha::Common::read_open( $file2 );
-
- @vals1 = Maasha::Common::get_fields( $fh1 );
- @vals2 = Maasha::Common::get_fields( $fh2 );
-
- while ( $num1 > 0 and $num2 > 0 )
- {
- undef $record;
-
- if ( $num ) {
- $cmp = $vals1[ 0 ] <=> $vals2[ 0 ];
- } else {
- $cmp = $vals1[ 0 ] cmp $vals2[ 0 ];
- }
-
- if ( $cmp < 0 )
- {
- if ( $merge =~ /^(AorB|AnotB)$/ )
- {
- for ( $i = 0; $i < @keys1; $i++ ) {
- $record->{ $keys1[ $i ] } = $vals1[ $i ];
- }
-
- put_record( $record, $out );
- }
-
- @vals1 = Maasha::Common::get_fields( $fh1 );
- $num1--;
- }
- elsif ( $cmp > 0 )
- {
- if ( $merge =~ /^(BorA|BnotA)$/ )
- {
- for ( $i = 0; $i < @keys2; $i++ ) {
- $record->{ $keys2[ $i ] } = $vals2[ $i ];
- }
-
- put_record( $record, $out );
- }
-
- @vals2 = Maasha::Common::get_fields( $fh2 );
- $num2--;
- }
- else
- {
- if ( $merge =~ /^(AandB|AorB|BorA)$/ )
- {
- for ( $i = 0; $i < @keys1; $i++ ) {
- $record->{ $keys1[ $i ] } = $vals1[ $i ];
- }
-
- for ( $i = 1; $i < @keys2; $i++ ) {
- $record->{ $keys2[ $i ] } = $vals2[ $i ];
- }
-
- put_record( $record, $out );
- }
-
- @vals1 = Maasha::Common::get_fields( $fh1 );
- @vals2 = Maasha::Common::get_fields( $fh2 );
- $num1--;
- $num2--;
- }
- }
-
- close $fh1;
- close $fh2;
-
- unlink $file1;
- unlink $file2;
-
- if ( $num1 > 0 and $merge =~ /^(AorB|AnotB)$/ )
- {
- undef $record;
-
- for ( $i = 0; $i < @keys1; $i++ ) {
- $record->{ $keys1[ $i ] } = $vals1[ $i ];
- }
-
- put_record( $record, $out );
- }
-
- if ( $num2 > 0 and $merge =~ /^(BorA|BnotA)$/ )
- {
- undef $record;
-
- for ( $i = 0; $i < @keys2; $i++ ) {
- $record->{ $keys2[ $i ] } = $vals2[ $i ];
- }
-
- 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 = { "RECORDS_COUNT" => $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;
-
- $tmp_file = "$BP_TMP/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 );
-
- $tmp_file = "$BP_TMP/count_cache.tmp";
-
- $fh_out = Maasha::Common::write_open( $tmp_file );
-
- $cache = 0;
- $num = 0;
-
- while ( $record = get_record( $in ) )
- {
- map { $count_hash{ $_ }{ $record->{ $_ } }++ if exists $record->{ $_ } } @{ $options->{ "keys" } };
-
- push @records, $record;
+use Getopt::Long qw( :config bundling );
+use Data::Dumper;
+use Maasha::Match;
+use Maasha::Common;
+use Maasha::Filesys;
+use vars qw( @ISA @EXPORT_OK );
- if ( scalar @records > 5_000_000 ) # too many records to hold in memory - use disk cache
- {
- map { put_record( $_, $fh_out ) } @records;
+require Exporter;
- undef @records;
+@ISA = qw( Exporter );
- $cache = 1;
- }
+@EXPORT_OK = qw(
+ read_stream
+ write_stream
+ get_record
+ put_record
+);
- print STDERR "verbose: records read $num\n" if ( $options->{ 'verbose' } and ( $num % 1_000_000 ) == 0 );
- $num++;
- }
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SIGNAL HANDLER <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
- close $fh_out;
- if ( $cache )
- {
- $num = 0;
+$SIG{ '__DIE__' } = \&sig_handler;
+$SIG{ 'INT' } = \&sig_handler;
+$SIG{ 'TERM' } = \&sig_handler;
- $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" } };
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
- put_record( $record, $out );
- print STDERR "verbose: cache read $num\n" if ( $options->{ 'verbose' } and ( $num % 1_000_000 ) == 0 );
+sub status_set
+{
+ my ( $time_stamp, $script, $user, $pid, $file, $fh );
- $num++;
- }
-
- close $fh_in;
- }
+ $time_stamp = Maasha::Common::time_stamp();
+ $user = Maasha::Common::get_user();
+ $script = Maasha::Common::get_scriptname();
+ $pid = Maasha::Common::get_processid();
- foreach $record ( @records )
- {
- map { $record->{ $_ . "_COUNT" } = $count_hash{ $_ }{ $record->{ $_ } } if exists $record->{ $_ } } @{ $options->{ "keys" } };
+ $file = bp_tmp() . "/" . join( ".", $user, $script, $pid ) . ".status";
+ $fh = Maasha::Filesys::file_write_open( $file );
+ flock($fh, 2);
- put_record( $record, $out );
- }
+ print $fh join( ";", $time_stamp, join( " ", @ARGV ) ) . "\n";
- unlink $tmp_file;
+ close $fh;
}
-sub script_plot_histogram
+sub status_log
{
- # Martin A. Hansen, September 2007.
+ # Martin A. Hansen, June 2009.
- # Plot a simple histogram for a given key using GNU plot.
+ # Retrieves initial status information written with status_set and uses this
+ # to write a status entry to the log file.
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
+ my ( $status, # status - OPTIONAL
) = @_;
# 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" };
- }
+ my ( $time0, $time1, $script, $user, $pid, $file, $fh, $elap, $fh_global, $fh_local, $line, $args, $tmp_dir );
- 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;
- }
+ $status ||= "OK";
- $result = Maasha::Plot::histogram_simple( \@data_list, $options );
+ $time1 = Maasha::Common::time_stamp();
+ $user = Maasha::Common::get_user();
+ $script = Maasha::Common::get_scriptname();
+ $pid = Maasha::Common::get_processid();
- $fh = write_stream( $options->{ "data_out" } );
+ $file = bp_tmp() . "/" . join( ".", $user, $script, $pid ) . ".status";
- print $fh "$_\n" foreach @{ $result };
+ return if not -f $file;
+ $fh = Maasha::Filesys::file_read_open( $file );
+ flock($fh, 1);
+ $line = <$fh>;
+ chomp $line;
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";
+ unlink $file;
- while ( $record = get_record( $in ) )
- {
- $data_hash{ $record->{ $options->{ "key" } } }++ if $record->{ $options->{ "key" } };
-
- put_record( $record, $out ) if not $options->{ "no_stream" };
- }
+ ( $time0, $args, $tmp_dir ) = split /;/, $line;
- $max = Maasha::Calc::list_max( [ keys %data_hash ] );
+ Maasha::Filesys::dir_remove( $tmp_dir ) if defined $tmp_dir;
- for ( $i = 0; $i < $max; $i++ ) {
- push @data_list, [ $i, $data_hash{ $i } || 0 ];
- }
+ $elap = Maasha::Common::time_stamp_diff( $time0, $time1 );
- $result = Maasha::Plot::histogram_lendist( \@data_list, $options );
+ $fh_global = Maasha::Filesys::file_append_open( "$ENV{ 'BP_LOG' }/biopieces.log" );
+ flock($fh_global, 2);
+ $fh_local = Maasha::Filesys::file_append_open( "$ENV{ 'HOME' }/.biopieces.log" );
+ flock($fh_local, 2);
- $fh = write_stream( $options->{ "data_out" } );
+ print $fh_global join( "\t", $time0, $time1, $elap, $user, $status, "$script $args" ) . "\n";
+ print $fh_local join( "\t", $time0, $time1, $elap, $user, $status, "$script $args" ) . "\n";
- print $fh "$_\n" foreach @{ $result };
+ $fh_global->autoflush( 1 );
+ $fh_local->autoflush( 1 );
- close $fh;
+ close $fh_global;
+ close $fh_local;
}
-sub script_plot_chrdist
+sub log_biopiece
{
- # Martin A. Hansen, August 2007.
-
- # Plot chromosome distribution using GNU plot.
+ # Martin A. Hansen, January 2008.
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
+ # Log messages to logfile.
# Returns nothing.
- my ( $record, %data_hash, @data_list, $elem, $sort_key, $count, $result, $fh );
-
- $options->{ "title" } ||= "Chromosome Distribution";
+ my ( $time_stamp, $user, $script, $fh );
- 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;
+ $time_stamp = Maasha::Common::time_stamp();
+ $user = Maasha::Common::get_user();
+ $script = Maasha::Common::get_scriptname();
- $result = Maasha::Plot::histogram_chrdist( \@data_list, $options );
+ $fh = Maasha::Filesys::file_append_open( "$ENV{ 'BP_LOG' }/biopieces.log" );
+ flock($fh, 2);
- $fh = write_stream( $options->{ "data_out" } );
+ print $fh "$time_stamp\t$user\t$script ", join( " ", @ARGV ), "\n";
- print $fh "$_\n" foreach @{ $result };
+ $fh->autoflush( 1 );
close $fh;
}
-sub script_plot_karyogram
+sub read_stream
{
- # Martin A. Hansen, August 2007.
+ # Martin A. Hansen, July 2007.
- # Plot hits on karyogram.
+ # Opens a stream to STDIN or a file,
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
+ my ( $file, # file - OPTIONAL
) = @_;
- # Returns nothing.
-
- my ( %options, $record, @data, $fh, $result, %data_hash );
-
- $options->{ "genome" } ||= "human";
- $options->{ "feat_color" } ||= "black";
+ # Returns filehandle.
- 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" } ];
- }
+ my ( $fh );
- put_record( $record, $out ) if not $options->{ "no_stream" };
+ if ( not -t STDIN ) {
+ $fh = Maasha::Filesys::stdin_read();
+ } elsif ( not $file ) {
+ # Maasha::Common::error( qq(no data stream) );
+ } else {
+ $fh = Maasha::Filesys::file_read_open( $file );
}
-
- $result = Maasha::Plot::karyogram( \%data_hash, \%options );
-
- $fh = write_stream( $options->{ "data_out" } );
-
- print $fh $result;
-
- close $fh;
+
+ return $fh;
}
-sub script_plot_matches
+sub write_stream
{
# Martin A. Hansen, August 2007.
- # Plot matches in 2D generating a dotplot.
+ # Opens a stream to STDOUT or a file.
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
+ my ( $path, # path - OPTIONAL
+ $gzip, # compress data - OPTIONAL
) = @_;
- # Returns nothing.
-
- my ( $record, @data, $fh, $result, %data_hash );
-
- $options->{ "direction" } ||= "both";
+ # Returns filehandle.
- 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;
- }
+ my ( $fh );
- put_record( $record, $out ) if not $options->{ "no_stream" };
+ if ( $path ) {
+ $fh = Maasha::Filesys::file_write_open( $path, $gzip );
+ } else {
+ $fh = Maasha::Filesys::stdout_write();
}
- $options->{ "title" } ||= "plot_matches";
- $options->{ "xlabel" } ||= $data[ 0 ]->{ "Q_ID" };
- $options->{ "ylabel" } ||= $data[ 0 ]->{ "S_ID" };
-
- $result = Maasha::Plot::dotplot_matches( \@data, $options, $BP_TMP );
-
- $fh = write_stream( $options->{ "data_out" } );
-
- print $fh "$_\n" foreach @{ $result };
-
- close $fh;
+ return $fh;
}
-sub script_length_vals
+sub close_stream
{
- # Martin A. Hansen, August 2007.
+ # Martin A. Hansen, May 2009.
- # Determine the length of the value for given keys.
+ # Close stream if open.
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
+ my ( $fh, # filehandle
) = @_;
# 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 );
- }
+ close $fh if defined $fh;
}
-sub script_sum_vals
+sub get_record
{
- # Martin A. Hansen, August 2007.
+ # Martin A. Hansen, July 2007.
- # Calculates the sums for values of given keys.
+ # Reads one record at a time and converts that record
+ # to a Perl data structure (a hash) which is returned.
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
+ my ( $fh, # handle to stream
) = @_;
- # 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.
+ # Returns a hash.
- # Calculate the mean of values of given keys.
+ my ( $block, @lines, $line, $key, $value, %record );
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
+ return if not defined $fh;
- # Returns nothing.
+ local $/ = "\n---\n";
- my ( $record, $key, %sum_hash, %count_hash, $mean, $fh );
+ $block = <$fh>;
- while ( $record = get_record( $in ) )
- {
- foreach $key ( @{ $options->{ "keys" } } )
- {
- if ( $record->{ $key } )
- {
- $sum_hash{ $key } += $record->{ $key };
- $count_hash{ $key }++;
- }
- }
+ return if not defined $block;
- put_record( $record, $out ) if not $options->{ "no_stream" };
- }
+ chomp $block;
- $fh = write_stream( $options->{ "data_out" } );
+ @lines = split "\n", $block;
- foreach $key ( @{ $options->{ "keys" } } )
+ foreach $line ( @lines )
{
- if ( $count_hash{ $key } ) {
- $mean = sprintf( "%.2f", ( $sum_hash{ $key } / $count_hash{ $key } ) );
- } else {
- $mean = "N/A";
- }
+ ( $key, $value ) = split ": ", $line, 2;
- put_record( { $key . "_MEAN" => $mean } , $fh );
+ $record{ $key } = $value;
}
- close $fh;
+ return wantarray ? %record : \%record;
}
-sub script_median_vals
+sub put_record
{
- # Martin A. Hansen, March 2008.
+ # Martin A. Hansen, July 2007.
- # Calculate the median values of given keys.
+ # Given a Perl datastructure (a hash ref) emits this to STDOUT or a filehandle.
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
+ my ( $data, # data structure
+ $fh, # file handle - OPTIONAL
) = @_;
# Returns nothing.
- my ( $record, $key, %median_hash, $median, $fh );
-
- while ( $record = get_record( $in ) )
+ if ( scalar keys %{ $data } )
{
- foreach $key ( @{ $options->{ "keys" } } ) {
- push @{ $median_hash{ $key } }, $record->{ $key } if defined $record->{ $key };
+ if ( $fh )
+ {
+ map { print $fh "$_: $data->{ $_ }\n" } keys %{ $data };
+ print $fh "---\n";
}
-
- 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 {
- $median = "N/A";
+ else
+ {
+ map { print "$_: $data->{ $_ }\n" } keys %{ $data };
+ print "---\n";
}
-
- put_record( { $key . "_MEDIAN" => $median } , $fh );
}
- close $fh;
+ undef $data;
}
-sub script_max_vals
+sub parse_options
{
- # 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 };
- }
- }
+ # Martin A. Hansen, May 2009
- 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 };
- }
+ # Parses and checks options for Biopieces.
- put_record( $max_record, $fh );
+ # First the argument list is checked for duplicates and then
+ # options are parsed from ARGV after which it is checked if
+ # the Biopieces usage information should be printed. Finally,
+ # all options from ARGV are checked according to the argument list.
- close $fh;
-}
+ my ( $arg_list, # data structure with argument description
+ ) = @_;
+ # Returns hashref.
-sub script_min_vals
-{
- # Martin A. Hansen, February 2008.
+ my ( $arg, @list, $options );
- # Determine the minimum values of given keys.
+ # ---- Adding the mandatory arguments to the arg_list ----
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
+ push @{ $arg_list }, (
+ { long => 'help', short => '?', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'stream_in', short => 'I', type => 'file!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'stream_out', short => 'O', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'verbose', short => 'v', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ );
- # Returns nothing.
+ check_duplicates_args( $arg_list );
- my ( $record, $key, $fh, %min_hash, $min_record );
+ # ---- Compiling options list ----
- while ( $record = get_record( $in ) )
+ foreach $arg ( @{ $arg_list } )
{
- 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 };
- }
- }
+ if ( $arg->{ 'type' } eq 'flag' ) {
+ push @list, "$arg->{ 'long' }|$arg->{ 'short' }";
+ } else {
+ push @list, "$arg->{ 'long' }|$arg->{ 'short' }=s";
}
-
- put_record( $record, $out ) if not $options->{ "no_stream" };
}
- $fh = write_stream( $options->{ "data_out" } );
+ # ---- Parsing options from @ARGV ----
+
+ $options = {};
+
+ Getopt::Long::GetOptions( $options, @list );
+
+ # print Dumper( $options );
+
+ check_print_usage( $options );
+
+ # ---- Expanding and checking options ----
- foreach $key ( @{ $options->{ "keys" } } )
+ foreach $arg ( @{ $arg_list } )
{
- $min_record->{ $key . "_MIN" } = $min_hash{ $key };
+ check_mandatory( $arg, $options );
+ set_default( $arg, $options );
+ check_uint( $arg, $options );
+ check_int( $arg, $options );
+ set_list( $arg, $options );
+ check_dir( $arg, $options );
+ check_file( $arg, $options );
+ set_files( $arg, $options );
+ check_files( $arg, $options );
+ check_allowed( $arg, $options );
+ check_disallowed( $arg, $options );
}
- put_record( $min_record, $fh );
+ # print Dumper( $options );
- close $fh;
+ # return wantarray ? $options : %{ $options }; # WTF! Someone changed the behaviour of wantarray???
+
+ return $options;
}
-sub script_upload_to_ucsc
+sub check_duplicates_args
{
- # Martin A. Hansen, August 2007.
-
- # Calculate the mean of values of given keys.
+ # Martin A. Hansen, May 2009
- # This routine has developed into the most ugly hack. Do something!
+ # Check if there are duplicate long or short arguments,
+ # and raise an error if so.
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
+ my ( $arg_list, # List of argument hashrefs,
) = @_;
# 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, $vals );
-
- $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.
+ my ( $arg, %check_hash );
- $file = "$BP_TMP/ucsc_upload.tmp";
+ foreach $arg ( @{ $arg_list } )
+ {
+ Maasha::Common::error( qq(Duplicate long argument: $arg->{ 'long' }) ) if exists $check_hash{ $arg->{ 'long' } };
+ Maasha::Common::error( qq(Duplicate short argument: $arg->{ 'short' }) ) if exists $check_hash{ $arg->{ 'short' } };
- $append = 0;
+ $check_hash{ $arg->{ 'long' } } = 1;
+ $check_hash{ $arg->{ 'short' } } = 1;
+ }
+}
- $first = 1;
- $i = 0;
+sub check_print_usage
+{
+ # Martin A. Hansen, May 2009.
- if ( $options->{ 'wiggle' } )
- {
- while ( $record = get_record( $in ) )
- {
- put_record( $record, $out ) if not $options->{ "no_stream" };
+ # Check if we need to print usage and print usage
+ # and exit if that is the case.
- $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" };
+ my ( $options, # option hash
+ ) = @_;
- $fh_hash{ $record->{ "CHR" } } = Maasha::Common::write_open( "$BP_TMP/$record->{ 'CHR' }" ) if not exists $fh_hash{ $record->{ "CHR" } };
+ # Returns nothing.
- $fh_out = $fh_hash{ $record->{ "CHR" } };
-
- Maasha::UCSC::bed_put_entry( $record, $fh_out, 5 );
- }
+ my ( %options, $help, $script, $wiki );
- map { close $_ } keys %fh_hash;
+ %options = %{ $options };
+ $help = $options{ 'help' };
+ delete $options{ 'help' };
- $fh_out = Maasha::Common::write_open( $file );
+ $script = Maasha::Common::get_scriptname();
- foreach $chr ( sort keys %fh_hash )
+ if ( $script ne 'print_wiki' )
+ {
+ if ( $help or -t STDIN )
{
- Maasha::Common::run( "bedSort", "$BP_TMP/$chr $BP_TMP/$chr" );
-
- $fh_in = Maasha::Common::read_open( "$BP_TMP/$chr" );
-
- undef $block;
-
- while ( $entry = Maasha::UCSC::bed_get_entry( $fh_in, 5 ) )
+ if ( not ( exists $options{ 'stream_in' } or $options{ 'data_in' } ) )
{
- $chr = $entry->{ 'CHR' };
- $beg = $entry->{ 'CHR_BEG' };
- $end = $entry->{ 'CHR_END' };
- $q_id = $entry->{ 'Q_ID' };
-
- if ( $options->{ "score" } ) {
- $clones = $entry->{ 'SCORE' };
- } if ( $q_id =~ /_(\d+)$/ ) {
- $clones = $1;
- } else {
- $clones = 1;
- }
-
- if ( $block )
+ if ( scalar keys %options == 0 )
{
- 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 );
+ $wiki = $ENV{ 'BP_DIR' } . "/bp_usage/$script.wiki";
+
+ if ( $help ) {
+ `print_wiki --data_in=$wiki --help`;
+ } elsif ( $script =~ /^(list_biopieces|list_genomes|list_mysql_databases|biostat)$/ ) {
+ return;
+ } else {
+ `print_wiki --data_in=$wiki`;
}
- }
-
- if ( not $block )
- {
- $beg_block = $beg;
- $max = $end;
- for ( $i = 0; $i < ( $end - $beg ); $i++ ) {
- $block->[ $i ] += $clones;
- }
+ exit;
}
}
-
- close $fh_in;
-
- Maasha::UCSC::fixedstep_put_entry( $chr, $beg_block, $block, $fh_out, $options->{ "log10" } );
-
- unlink "$BP_TMP/$chr";
}
-
- close $fh_out;
-
- $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 "fixed_step" )
- {
- $vals = $record->{ "VALS" };
- $vals =~ tr/,/\n/;
+}
- print $fh_out "fixedStep chrom=$record->{ 'CHR' } start=$record->{ 'CHR_BEG' } step=$record->{ 'STEP' }\n";
- print $fh_out "$vals\n";
- $format = "WIGGLE" if not $format;
- }
- elsif ( $record->{ "REC_TYPE" } eq "PSL" )
- {
- Maasha::UCSC::psl_put_header( $fh_out ) if $first;
- Maasha::UCSC::psl_put_entry( $record, $fh_out );
-
- $first = 0;
+sub check_mandatory
+{
+ # Martin A. Hansen, May 2009.
- $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" } );
+ # Check if mandatory arguments are set and raises an error if not.
- $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 );
+ my ( $arg, # hashref
+ $options, # options hash
+ ) = @_;
- $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;
+ # Returns nothing.
- $format = "BED" if not $format;
- $columns = 6 if not $columns;
+ if ( $arg->{ 'mandatory' } eq 'yes' and not defined $options->{ $arg->{ 'long' } } ) {
+ Maasha::Common::error( qq(Argument --$arg->{ 'long' } is mandatory) );
+ }
+}
- 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;
+sub set_default
+{
+ # Martin A. Hansen, May 2009.
- Maasha::UCSC::bed_put_entry( $record, $fh_out, 6 );
- }
+ # Set default values in option hash.
- if ( $i == $options->{ "chunk_size" } )
- {
- close $fh_out;
+ my ( $arg, # hashref
+ $options, # options hash
+ ) = @_;
- if ( $format eq "BED" ) {
- Maasha::UCSC::bed_upload_to_ucsc( $BP_TMP, $file, $options, $append );
- } elsif ( $format eq "PSL" ) {
- Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
- }
+ # Returns nothing.
- unlink $file;
+ if ( not defined $options->{ $arg->{ 'long' } } ) {
+ $options->{ $arg->{ 'long' } } = $arg->{ 'default' }
+ }
+}
- $first = 1;
- $append = 1;
+sub check_uint
+{
+ # Martin A. Hansen, May 2009.
- $fh_out = Maasha::Common::write_open( $file );
- }
+ # Check if value to argument is an unsigned integer and
+ # raises an error if not.
- $i++;
- }
- }
+ my ( $arg, # hashref
+ $options, # options hash
+ ) = @_;
- close $fh_out;
+ # Returns nothing.
- if ( exists $options->{ "database" } and $options->{ "table" } )
+ if ( $arg->{ 'type' } eq 'uint' and defined $options->{ $arg->{ 'long' } } )
{
- if ( $format eq "BED" )
- {
- $type = "bed $columns";
-
- Maasha::UCSC::bed_upload_to_ucsc( $BP_TMP, $file, $options, $append );
- }
- elsif ( $format eq "BED_SS" )
- {
- $options->{ "sec_struct" } = 1;
-
- $type = "sec_struct";
-
- Maasha::UCSC::bed_upload_to_ucsc( $BP_TMP, $file, $options, $append );
- }
- elsif ( $format eq "PSL" )
- {
- $type = "psl";
-
- Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append );
+ if ( $options->{ $arg->{ 'long' } } !~ /^\d+$/ ) {
+ Maasha::Common::error( qq(Argument --$arg->{ 'long' } must be an unsigned integer - not $options->{ $arg->{ 'long' } }) );
}
- elsif ( $format eq "WIGGLE" )
- {
- $options->{ "visibility" } = "full";
-
- $wig_file = "$options->{ 'table' }.wig";
- $wib_file = "$options->{ 'table' }.wib";
-
- $wib_dir = "$ENV{ 'HOME' }/ucsc/wib";
+ }
+}
- Maasha::Common::dir_create_if_not_exists( $wib_dir );
- `cd $BP_TMP && wigEncode $file $wig_file $wib_file > /dev/null 2>&1`;
- Maasha::Common::run( "mv", "$BP_TMP/$wib_file $wib_dir" );
+sub check_int
+{
+ # Martin A. Hansen, May 2009.
- unlink $file;
+ # Check if value to argument is an integer and
+ # raises an error if not.
- $file = $wig_file;
+ my ( $arg, # hashref
+ $options, # options hash
+ ) = @_;
- $type = "wig 0";
+ # Returns nothing.
- Maasha::UCSC::wiggle_upload_to_ucsc( $BP_TMP, $wib_dir, $file, $options );
+ if ( $arg->{ 'type' } eq 'int' and defined $options{ $arg->{ 'long' } } )
+ {
+ if ( $options->{ $arg->{ 'long' } } !~ /^-?\d+$/ ) {
+ Maasha::Common::error( qq(Argument --$arg->{ 'long' } must be an integer - not $options->{ $arg->{ 'long' } }) );
}
-
- unlink $file;
-
- Maasha::UCSC::update_my_tracks( $options, $type );
}
}
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub record2fasta
+sub set_list
{
- # Martin A. Hansen, July 2008.
+ # Martin A. Hansen, May 2009.
- # Given a biopiece record converts it to a FASTA record.
- # If no generic SEQ or SEQ_NAME is found, the Q_* and S_* are
- # tried in that order.
+ # Splits an argument of type 'list' into a list that is put
+ # in the options hash.
- my ( $record, # record
+ my ( $arg, # hashref
+ $options, # options hash
) = @_;
- # Returns a tuple.
-
- my ( $seq_name, $seq );
-
- $seq_name = $record->{ "SEQ_NAME" } || $record->{ "Q_ID" } || $record->{ "S_ID" };
- $seq = $record->{ "SEQ" } || $record->{ "Q_SEQ" } || $record->{ "S_SEQ" };
+ # Returns nothing.
- if ( defined $seq_name and defined $seq ) {
- return wantarray ? ( $seq_name, $seq ) : [ $seq_name, $seq ];
- } else {
- return;
+ if ( $arg->{ 'type' } eq 'list' and defined $options->{ $arg->{ 'long' } } ) {
+ $options->{ $arg->{ 'long' } } = [ split /,/, $options->{ $arg->{ 'long' } } ];
}
}
-sub read_stream
+sub check_dir
{
- # Martin A. Hansen, July 2007.
+ # Martin A. Hansen, May 2009.
- # Opens a stream to STDIN or a file,
+ # Check if an argument of type 'dir!' truly is a directory and
+ # raises an error if not.
- my ( $path, # path - OPTIONAL
+ my ( $arg, # hashref
+ $options, # options hash
) = @_;
- # Returns filehandle.
-
- my ( $fh );
+ # Returns nothing.
- 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 );
+ if ( $arg->{ 'type' } eq 'dir!' and defined $options->{ $arg->{ 'long' } } )
+ {
+ if ( not -d $options->{ $arg->{ 'long' } } ) {
+ Maasha::Common::error( qq(No such directory: "$options->{ $arg->{ 'long' } }") );
+ }
}
-
-# $fh->autoflush(1) if $fh; # Disable file buffer for debugging.
-
- return $fh;
}
-sub write_stream
+sub check_file
{
- # Martin A. Hansen, August 2007.
+ # Martin A. Hansen, May 2009.
- # Opens a stream to STDOUT or a file.
+ # Check if an argument of type 'file!' truly is a file and
+ # raises an error if not.
- my ( $path, # path - OPTIONAL
- $gzip, # compress data - OPTIONAL
+ my ( $arg, # hashref
+ $options, # options hash
) = @_;
- # Returns filehandle.
-
- my ( $fh );
+ # Returns nothing.
- if ( $path ) {
- $fh = Maasha::Common::write_open( $path, $gzip );
- } else {
- $fh = Maasha::Common::write_stdout();
+ if ( $arg->{ 'type' } eq 'file!' and defined $options->{ $arg->{ 'long' } } )
+ {
+ if ( not -f $options->{ $arg->{ 'long' } } ) {
+ Maasha::Common::error( qq(No such file: "$options->{ $arg->{ 'long' } }") );
+ }
}
-
- return $fh;
}
-sub get_record
+sub set_files
{
- # Martin A. Hansen, July 2007.
+ # Martin A. Hansen, May 2009.
- # Reads one record at a time and converts that record
- # to a Perl data structure (a hash) which is returned.
+ # Split the argument to 'files' into a list that is put on the options hash.
- my ( $fh, # handle to stream
+ my ( $arg, # hashref
+ $options, # options hash
) = @_;
- # Returns a hash.
+ # Returns nothing.
- my ( $block, @lines, $line, $key, $value, %record );
+ if ( $arg->{ 'type' } eq 'files' and defined $options->{ $arg->{ 'long' } } ) {
+ $options->{ $arg->{ 'long' } } = [ split /,/, $options->{ $arg->{ 'long' } } ];
+ }
+}
- local $/ = "\n---\n";
- $block = <$fh>;
+sub check_files
+{
+ # Martin A. Hansen, May 2009.
- chomp $block;
+ # Split the argument to 'files!' and check if each file do exists before adding
+ # the file list to the options hash.
- return if not defined $block;
+ my ( $arg, # hashref
+ $options, # options hash
+ ) = @_;
- @lines = split "\n", $block;
+ # Returns nothing.
- foreach $line ( @lines )
+ my ( $elem, @files );
+
+ if ( $arg->{ 'type' } eq 'files!' and defined $options->{ $arg->{ 'long' } } )
{
- ( $key, $value ) = split ": ", $line, 2;
+ foreach $elem ( split /,/, $options->{ $arg->{ 'long' } } )
+ {
+ if ( -f $elem ) {
+ push @files, $elem;
+ } elsif ( $elem =~ /\*/ ) {
+ push @files, glob( $elem );
+ }
+ }
- $record{ $key } = $value;
- }
+ if ( scalar @files == 0 ) {
+ Maasha::Common::error( qq(Argument to --$arg->{ 'long' } must be a valid file or fileglob expression - not $options->{ $arg->{ 'long' } }) );
+ }
- return wantarray ? %record : \%record;
+ $options->{ $arg->{ 'long' } } = [ @files ];
+ }
}
-sub put_record
+sub check_allowed
{
- # Martin A. Hansen, July 2007.
+ # Martin A. Hansen, May 2009.
- # Given a Perl datastructure (a hash ref) emits this to STDOUT or a filehandle.
+ # Check if all values to all arguement are allowed and raise an
+ # error if not.
- my ( $data, # data structure
- $fh, # file handle - OPTIONAL
+ my ( $arg, # hashref
+ $options, # options hash
) = @_;
# Returns nothing.
- if ( scalar keys %{ $data } )
+ my ( $elem );
+
+ if ( defined $arg->{ 'allowed' } and defined $options->{ $arg->{ 'long' } } )
{
- if ( $fh )
+ map { $val_hash{ $_ } = 1 } split /,/, $arg->{ 'allowed' };
+
+ if ( $arg->{ 'type' } =~ /^(list|files|files!)$/ )
{
- map { print $fh "$_: $data->{ $_ }\n" } keys %{ $data };
- print $fh "---\n";
+ foreach $elem ( @{ $options->{ $arg->{ 'long' } } } )
+ {
+ if ( not exists $val_hash{ $elem } ) {
+ Maasha::Common::error( qq(Argument to --$arg->{ 'long' } $elem is not allowed) );
+ }
+ }
}
else
{
- map { print "$_: $data->{ $_ }\n" } keys %{ $data };
- print "---\n";
+ if ( not exists $val_hash{ $options->{ $arg->{ 'long' } } } ) {
+ Maasha::Common::error( qq(Argument to --$arg->{ 'long' } $options->{ $arg->{ 'long' } } is not allowed) );
+ }
}
}
-
- undef $data;
}
-sub getopt_files
+sub check_disallowed
{
- # Martin A. Hansen, November 2007.
+ # Martin A. Hansen, May 2009.
- # 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
+ # Check if any values to all arguemnts are disallowed and raise an error if so.
- my ( $option, # option from GetOpt::Long
+ my ( $arg, # hashref
+ $options, # options hash
) = @_;
- # Returns a list.
+ # Returns nothing.
- my ( $elem, @files );
+ my ( $val, %val_hash );
- foreach $elem ( split ",", $option )
+ if ( defined $arg->{ 'disallowed' } and defined $options->{ $arg->{ 'long' } } )
{
- if ( -f $elem ) {
- push @files, $elem;
- } elsif ( $elem =~ /\*/ ) {
- push @files, glob( $elem );
+ foreach $val ( split /,/, $arg->{ 'disallowed' } )
+ {
+ if ( $options->{ $arg->{ 'long' } } eq $val ) {
+ Maasha::Common::error( qq(Argument to --$arg->{ 'long' } $val is disallowed) );
+ }
}
}
-
- return wantarray ? @files : \@files;
}
+# marked for deletion - obsolete?
+#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( $elem );
+# }
+# }
+#
+# return wantarray ? @files : \@files;
+#}
+
+
sub sig_handler
{
# Martin A. Hansen, April 2008.
# print STDERR "signal->$sig<-\n";
+ my $script = Maasha::Common::get_scriptname();
+
chomp $sig;
sleep 1;
- if ( -d $BP_TMP )
+ if ( $sig =~ /MAASHA_ERROR/ )
{
- 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";
- }
-
- clean_tmp();
+ print STDERR "\nProgram '$script' had an error" . " - Please wait for temporary data to be removed\n";
+ status_log( "ERROR" );
+ }
+ elsif ( $sig eq "INT" )
+ {
+ print STDERR "\nProgram '$script' interrupted (ctrl-c was pressed)" . " - Please wait for temporary data to be removed\n";
+ status_log( "INTERRUPTED" );
+ }
+ elsif ( $sig eq "TERM" )
+ {
+ print STDERR "\nProgram '$script' terminated (someone used kill?)" . " - Please wait for temporary data to be removed\n";
+ status_log( "TERMINATED" );
}
+ else
+ {
+ print STDERR "\nProgram '$script' died->$sig" . " - Please wait for temporary data to be removed\n";
+ status_log( "DIED" );
+ }
+
+ clean_tmp();
exit( 0 );
}
{
# Martin A. Hansen, July 2008.
- # Cleans out any unused temporary files and direcotries in BP_TMP.
+ # Cleans out any unused temporary files and directories in BP_TMP.
# Returns nothing.
my ( $tmpdir, @dirs, $curr_pid, $dir, $user, $sid, $pid );
- $tmpdir = $ENV{ 'BP_TMP' } || Maasha::Common::error( 'No BP_TMP variable in environment.' );
+ $tmpdir = bp_tmp();
$curr_pid = Maasha::Common::get_processid();
- @dirs = Maasha::Common::ls_dirs( $tmpdir );
+ @dirs = Maasha::Filesys::ls_dirs( $tmpdir );
foreach $dir ( @dirs )
{
$sid = $2;
$pid = $3;
+# next if $user eq "maasha"; # DEBUG
+
if ( $user eq Maasha::Common::get_user() )
{
if ( not Maasha::Common::process_running( $pid ) )
{
# print STDERR "Removing stale dir: $dir\n";
- Maasha::Common::dir_remove( $dir );
+ Maasha::Filesys::dir_remove( $dir );
}
elsif ( $pid == $curr_pid )
{
# print STDERR "Removing current dir: $dir\n";
- Maasha::Common::dir_remove( $dir );
+ Maasha::Filesys::dir_remove( $dir );
}
}
}
}
+sub get_tmpdir
+{
+ # Martin A. Hansen, April 2008.
+
+ # Create a temporary directory based on
+ # $ENV{ 'BP_TMP' } and sessionid. The directory
+ # name is written to the status file.
+
+ # Returns a path.
+
+ my ( $user, $sid, $pid, $script, $path, $file, $fh, $line );
+
+ $user = Maasha::Common::get_user();
+ $sid = Maasha::Common::get_sessionid();
+ $pid = Maasha::Common::get_processid();
+ $script = Maasha::Common::get_scriptname();
+
+ $path = bp_tmp() . "/" . join( "_", $user, $sid, $pid, "bp_tmp" );
+ $file = bp_tmp() . "/" . join( ".", $user, $script, $pid ) . ".status";
+
+ $fh = Maasha::Filesys::file_read_open( $file );
+ flock($fh, 1);
+ $line = <$fh>;
+ chomp $line;
+ close $fh;
+
+ $fh = Maasha::Filesys::file_write_open( $file );
+ flock($fh, 2);
+ print $fh "$line;$path\n";
+ close $fh;
+
+ Maasha::Filesys::dir_create( $path );
+
+ return $path;
+}
+
+
+sub biopiecesrc
+{
+ # Martin A. Hansen, July 2009.
+
+ # Read Biopiece configuration info from .biopiecesrc.
+ # and returns the value of a given key.
+
+ my ( $key, # configuration key
+ ) = @_;
+
+ # Returns a string.
+
+ my ( $file, $fh, $record );
+
+ $file = "$ENV{ 'HOME' }/.biopiecesrc";
+
+ return undef if not -f $file;
+
+ $fh = Maasha::Filesys::file_read_open( $file );
+ flock($fh, 1);
+ $record = get_record( $fh );
+ close $fh;
+
+ if ( exists $record->{ $key } ) {
+ return $record->{ $key };
+ } else {
+ return undef;
+ }
+}
+
+sub bp_tmp
+{
+ # Martin A. Hansen, March 2013.
+
+ # Returns the BP_TMP path.
+ # Errs if no BP_TMP in ENV and
+ # creates BP_TMP if it doesn't exists.
+
+ my ( $path );
+
+ Maasha::Common::error( qq(no BP_TMP set in %ENV) ) if not -d $ENV{ 'BP_TMP' };
+
+ $path = $ENV{ 'BP_TMP' };
+
+ unless ( -d $path ) { # No BP_TMP so we create it
+ mkdir $path or die qq(failed to create dir "$path": $!);
+ }
+
+ return $path;
+}
+
END
{
clean_tmp();
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
1;
__END__
projects / biopieces.git / blobdiff