From 69594d8d5d38c83d32cd3b57ac3388af89db1ee4 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Mon, 25 May 2009 07:40:26 +0000 Subject: [PATCH] migrated blat_seq git-svn-id: http://biopieces.googlecode.com/svn/trunk@406 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/blat_seq | 135 ++++++++++++++++++++++++++++++++++- code_perl/Maasha/BioRun.pm | 79 +------------------- code_perl/Maasha/UCSC/PSL.pm | 12 ++-- 3 files changed, 139 insertions(+), 87 deletions(-) diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq index fdf5bd2..bc5af18 100755 --- a/bp_bin/blat_seq +++ b/bp_bin/blat_seq @@ -1,6 +1,135 @@ -#!/usr/bin/env perl +#!/usr/bin/env perl -w + +# 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 +# as published by the Free Software Foundation; either version 2 +# of the License, or (at your option) any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +# http://www.gnu.org/copyleft/gpl.html + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# BLAT sequences in the stream against a genome. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Filesys; +use Maasha::Fasta; +use Maasha::Seq; +use Maasha::UCSC::PSL; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $blat_args, $genome_file, $query_file, $fh_in, $fh_out, + $tmp_dir, $type, $result_file, $entry ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { long => 'occ', short => 'c', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'tile_size', short => 't', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 }, + { long => 'step_size', short => 's', type => 'uint', mandatory => 'no', default => 11, allowed => undef, disallowed => 0 }, + { long => 'min_identity', short => 'm', type => 'uint', mandatory => 'no', default => 90, allowed => undef, disallowed => 0 }, + { long => 'min_score', short => 'M', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef }, + { long => 'one_off', short => 'o', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +$genome_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/fasta/$options->{ 'genome' }.fna"; + +$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 $options->{ 'ooc' }; + +$tmp_dir = Maasha::Biopieces::get_tmpdir(); +$query_file = "$tmp_dir/blat.seq"; + +$fh_out = Maasha::Filesys::file_write_open( $query_file ); + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) + { + $type = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } ) if not $type; + Maasha::Fasta::put_entry( $entry, $fh_out, 80 ); + } + + Maasha::Biopieces::put_record( $record, $out ); +} + +close $fh_out; + +$blat_args .= " -t=dnax" if $type eq "protein"; +$blat_args .= " -q=$type"; + +$result_file = "$tmp_dir/blat.psl"; + +Maasha::Common::run( "blat", "$genome_file $query_file $blat_args $result_file > /dev/null 2>&1" ); + +unlink $query_file; + +$fh_in = Maasha::Filesys::file_read_opem( $result_file ); + +while ( $entry = Maasha::UCSC::PSL::psl_entry_get( $fh_in ) ) +{ + if ( $record = Maasha::UCSC::PSL::psl2biopiece( $entry ) ) { + Maasha::Biopieces::put_record( $record, $out ); + } +} + +close $fh_in; +unlink $result_file; + +Maasha::Filesys::dir_remove( $tmp_dir ); + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +BEGIN +{ + $run_time_beg = Maasha::Biopieces::run_time(); + + Maasha::Biopieces::log_biopiece(); +} + + +END +{ + Maasha::Biopieces::close_stream( $in ); + Maasha::Biopieces::close_stream( $out ); + + $run_time_end = Maasha::Biopieces::run_time(); + + Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ -use Maasha::BioRun; diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index d9973a8..ef48911 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -147,7 +147,6 @@ sub run_script 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 "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 ) } @@ -423,18 +422,6 @@ sub get_options genome|g=s ); } - 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( @@ -858,7 +845,7 @@ sub get_options Maasha::Common::error( qq(no --index_name specified) ) if $script =~ /create_vmatch_index/ and not $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 =~ /get_genome_align|get_genome_phastcons|blat_seq|plot_phastcons_profiles|plot_karyogram/ and not $options{ "genome" }; + Maasha::Common::error( qq(no --genome specified) ) if $script =~ /get_genome_align|get_genome_phastcons|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" }; @@ -2475,70 +2462,6 @@ sub script_patscan_seq } -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 = Maasha::Biopieces::get_record( $in ) ) - { - if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) - { - $type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not $type; - Maasha::Fasta::put_entry( $entry, $fh_out, 80 ); - } - - Maasha::Biopieces::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 { Maasha::Biopieces::put_record( $_, $out ) } @{ $entries }; - - unlink $result_file; -} - - sub script_soap_seq { # Martin A. Hansen, July 2008. diff --git a/code_perl/Maasha/UCSC/PSL.pm b/code_perl/Maasha/UCSC/PSL.pm index a45006e..4dfaf84 100644 --- a/code_perl/Maasha/UCSC/PSL.pm +++ b/code_perl/Maasha/UCSC/PSL.pm @@ -120,7 +120,7 @@ sub psl_entry_get } -sub psl2record +sub psl2biopiece { # Martin A. Hansen, November 2008 @@ -179,11 +179,11 @@ sub psl_calc_score my ( $score ); - $score = $psl_entry[ MATCHES ] + - int( $psl_entry[ REPMATCHES ] / 2 ) - - $psl_entry[ MISMATCHES ] - - $psl_entry[ QNUMINSERT ] - - $psl_entry[ SNUMINSERT ]; + $score = $psl_entry->[ MATCHES ] + + int( $psl_entry->[ REPMATCHES ] / 2 ) - + $psl_entry->[ MISMATCHES ] - + $psl_entry->[ QNUMINSERT ] - + $psl_entry->[ SNUMINSERT ]; return $score; } -- 2.39.5