From 69594d8d5d38c83d32cd3b57ac3388af89db1ee4 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
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