From: martinahansen Date: Mon, 28 Sep 2009 16:29:54 +0000 (+0000) Subject: added bwa_seq X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=b4039cd22036599a2ea32211ff50f20cc9345eab;p=biopieces.git added bwa_seq git-svn-id: http://biopieces.googlecode.com/svn/trunk@685 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq index 2b9254d..dc8b09e 100755 --- a/bp_bin/bowtie_seq +++ b/bp_bin/bowtie_seq @@ -21,7 +21,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -# Use bowtie to map sequences in the stream against a specified genome. +# Use bowtie to map sequences in the stream against a specified genome or index. # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @@ -51,7 +51,7 @@ $options = Maasha::Biopieces::parse_options( ] ); -Maasha::Common::error( qq(both --index_hame and --genome specified) ) if $options->{ "genome" } and $options->{ "index_name" }; +Maasha::Common::error( qq(both --index_name and --genome specified) ) if $options->{ "genome" } and $options->{ "index_name" }; Maasha::Common::error( qq(no --index_name or --genome specified) ) if not $options->{ "genome" } and not $options->{ "index_name" }; $in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); diff --git a/bp_bin/bwa_seq b/bp_bin/bwa_seq new file mode 100755 index 0000000..c712b8f --- /dev/null +++ b/bp_bin/bwa_seq @@ -0,0 +1,138 @@ +#!/usr/bin/env perl + +# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Use BWA to map sequences in the stream against a specified genome or index. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +use warnings; +use strict; +use Data::Dumper; +use Maasha::Biopieces; +use Maasha::Common; +use Maasha::Fastq; +use Maasha::SAM; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $options, $in, $out, $index, $tmp_dir, $tmp_fq, $tmp_sai, $tmp_sam, $fh_in, $fh_out, $record, $entry, $line, @fields, $type, @args, $arg ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'index_name', short => 'i', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'mismatches', short => 'm', type => 'uint', mandatory => 'no', default => 0, allowed => "0,1,2,3", disallowed => undef }, + { long => 'max_hits', short => 'h', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + { long => 'cpus', short => 'c', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 }, + ] +); + +Maasha::Common::error( qq(both --index_name and --genome specified) ) if $options->{ "genome" } and $options->{ "index_name" }; +Maasha::Common::error( qq(no --index_name or --genome specified) ) if not $options->{ "genome" } and not $options->{ "index_name" }; + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +if ( defined $options->{ 'genome' } ) { + $index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }"; +} elsif (defined $options->{ 'index_name' } ) { + $index = $options->{ 'index_name' }; +} + +$tmp_dir = Maasha::Biopieces::get_tmpdir(); +$tmp_fq = "$tmp_dir/bwa.fq"; +$tmp_sai = "$tmp_dir/bwa.fq.sai"; +$tmp_sam = "$tmp_dir/bwa.fq.sam"; + +$fh_out = Maasha::Filesys::file_write_open( $tmp_fq ); + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + if ( $entry = Maasha::Fastq::biopiece2fastq( $record ) ) { + Maasha::Fastq::put_entry( $entry, $fh_out ); + } + + Maasha::Biopieces::put_record( $record, $out ); +} + +close $fh_out; + +push @args, "-t $options->{ 'cpus' }"; +push @args, "-R $options->{ 'max_hits' }" if $options->{ 'max_hits' }; + +$arg = join " ", @args; + +if ( $options->{ 'verbose' } ) +{ + print STDERR qq(Running: bwa aln $arg $index $tmp_fq > $tmp_sai\n); + Maasha::Common::run( "bwa", "aln $arg $index $tmp_fq > $tmp_sai" ); + print STDERR qq(Running: bwa samse $index $tmp_sai $tmp_fq > $tmp_sam\n); + Maasha::Common::run( "bwa", "samse $index $tmp_sai $tmp_fq > $tmp_sam" ) +} +else +{ + Maasha::Common::run( "bwa", "aln $arg $index $tmp_fq > $tmp_sai 2> /dev/null" ); + Maasha::Common::run( "bwa", "samse $index $tmp_sai $tmp_fq > $tmp_sam 2> /dev/null" ); +} + +$fh_in = Maasha::Filesys::file_read_open( $tmp_sam ); + +while ( $entry = Maasha::SAM::get_entry( $fh_in ) ) +{ + if ( $record = Maasha::SAM::sam2biopiece( $entry ) ) { + Maasha::Biopieces::put_record( $record, $out ); + } +} + +close $fh_in; + +unlink $tmp_fq; +unlink $tmp_sai; +unlink $tmp_sam; + +Maasha::Biopieces::close_stream( $in ); +Maasha::Biopieces::close_stream( $out ); + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +BEGIN +{ + Maasha::Biopieces::status_set(); +} + + +END +{ + Maasha::Biopieces::status_log(); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ diff --git a/code_perl/Maasha/Matrix.pm b/code_perl/Maasha/Matrix.pm index ed90a25..5d340f3 100644 --- a/code_perl/Maasha/Matrix.pm +++ b/code_perl/Maasha/Matrix.pm @@ -181,12 +181,60 @@ sub matrix_flip } } - $matrix = $AoA; + @{ $matrix } = @{ $AoA }; return wantarray ? @{ $matrix } : $matrix; } +sub matrix_deflate_rows +{ + # Martin A. Hansen, September 2009. + + # Reduces the number of elements in all rows, + # by collectiong elements in buckets that are + # averaged. + + my ( $matrix, # AoA data structure + $new_size + ) = @_; + + # Returns nothing. + + my ( $row ); + + foreach $row ( @{ $matrix } ) { + list_deflate( $row, $new_size ); + } +} + + +sub matrix_deflate_cols +{ + # Martin A. Hansen, September 2009. + + # Reduces the number of elements in all columns, + # by collectiong elements in buckets that are + # averaged. + + my ( $matrix, # AoA data structure + $new_size + ) = @_; + + # Returns nothing. + + my ( $col ); + + matrix_flip( $matrix ); + + foreach $col ( @{ $matrix } ) { + list_deflate( $col, $new_size ); + } + + matrix_flip( $matrix ); +} + + sub matrix_rotate_right { # Martin A. Hansen, April 2007 @@ -443,7 +491,7 @@ sub col_get sub cols_get { - # Martin A. Hansen, April 2007 + # Martin A. Hansen, April 2007. # returns a range of requested columns from a given matrix @@ -913,8 +961,8 @@ sub list_deflate # Defaltes a list of values to a specified size # and at the same time average the values. - my ( $list, - $new_size, + my ( $list, # list to deflate + $new_size, # new number of elements in list ) = @_; # Returns nothing. @@ -928,8 +976,6 @@ sub list_deflate $bucket_size = int( $old_size / $new_size ); $bucket_rest = $old_size - ( $new_size * $bucket_size ); - print STDERR "old_size: $old_size new_size: $new_size bucket_size: $bucket_size bucket_rest: $bucket_rest\n"; - $i = 0; while ( $i < $new_size ) diff --git a/code_perl/Maasha/Plot.pm b/code_perl/Maasha/Plot.pm index a662fbc..682c46f 100644 --- a/code_perl/Maasha/Plot.pm +++ b/code_perl/Maasha/Plot.pm @@ -97,11 +97,8 @@ sub lineplot_simple for ( $i = 1; $i < scalar @{ $data->[ 0 ] } + 1; $i++ ) { - if ( ( $i % 5 ) == 0 ) - { - $title = $options->{ 'keys' }->[ $i - 1 ] || $options->{ 'list' }; - push @plot_cmd, qq("$tmp_file" using $i with lines title "$title"); - } + $title = $options->{ 'keys' }->[ $i - 1 ] || $options->{ 'list' } || ""; + push @plot_cmd, qq("$tmp_file" using $i with lines title "$title"); } print $fh_in "plot " . join( ", ", @plot_cmd ) . "\n";