From: martinahansen Date: Thu, 23 Jul 2009 13:23:20 +0000 (+0000) Subject: added create_bowtie_index X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=15fc1cc28abfb41e8630c731fd6459dcdcd08e10;p=biopieces.git added create_bowtie_index git-svn-id: http://biopieces.googlecode.com/svn/trunk@584 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq index aedf02a..f7229f1 100755 --- a/bp_bin/bowtie_seq +++ b/bp_bin/bowtie_seq @@ -42,18 +42,26 @@ my ( $options, $in, $out, $index, $tmp_dir, $tmp_in, $tmp_out, $fh_in, $fh_out, $options = Maasha::Biopieces::parse_options( [ - { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', 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 => 'seed_length', short => 's', type => 'uint', mandatory => 'no', default => 28, allowed => undef, disallowed => 0 }, - { long => 'cpus', short => 'c', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 }, + { 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 => 'seed_length', short => 's', type => 'uint', mandatory => 'no', default => 28, allowed => undef, disallowed => 0 }, + { long => 'cpus', short => 'c', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 }, ] ); +Maasha::Common::error( qq(both --index_hame 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( $options->{ "stream_out" } ); -$index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }"; +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(); $tmp_in = "$tmp_dir/bowtie.seq"; diff --git a/bp_bin/create_bowtie_index b/bp_bin/create_bowtie_index new file mode 100755 index 0000000..b8949ea --- /dev/null +++ b/bp_bin/create_bowtie_index @@ -0,0 +1,100 @@ +#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Create a Bowtie index from sequences in stream for use with [bowtie_seq]. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +use warnings; +use strict; +use Maasha::Common; +use Maasha::Biopieces; +use Maasha::Bowtie; +use Maasha::Filesys; +use Maasha::Fasta; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $default, $formats, $options, $in, $out, $record, $tmp_dir, $file_tmp, $fh_tmp, $entry ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + ] +); + +Maasha::Common::error( qw(directory already exists: "$options->{ 'index_name' }") ) if -d $options->{ 'index_name' }; + +Maasha::Filesys::dir_create_if_not_exists( $options->{ 'index_name' } ); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +$tmp_dir = Maasha::Biopieces::get_tmpdir(); +$file_tmp = "$tmp_dir/create_bowtie_index.seq"; +$fh_tmp = Maasha::Filesys::file_write_open( $file_tmp ); + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) { + Maasha::Fasta::put_entry( $entry, $fh_tmp ); + } + + Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; +} + +close $fh_tmp; + +Maasha::Bowtie::bowtie_index( $file_tmp, $options->{ 'index_name' }, $options->{ 'index_name' }, $options->{ 'verbose' } ); + +unlink $file_tmp; + +Maasha::Filesys::dir_remove( $tmp_dir ); + +Maasha::Biopieces::close_stream( $in ); +Maasha::Biopieces::close_stream( $out ); + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +BEGIN +{ + Maasha::Biopieces::status_set(); +} + + +END +{ + Maasha::Biopieces::status_log(); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ diff --git a/bp_bin/format_genome b/bp_bin/format_genome index 9972bf5..af7de5c 100755 --- a/bp_bin/format_genome +++ b/bp_bin/format_genome @@ -30,6 +30,7 @@ use warnings; use strict; use Maasha::Fasta; use Maasha::Biopieces; +use Maasha::Bowtie; use Maasha::NCBI; use Maasha::Match; use Maasha::UCSC; @@ -115,7 +116,7 @@ foreach $format ( @{ $options->{ 'formats' } } ) elsif ( $format =~ /^blast$/i ) { Maasha::NCBI::blast_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/blast", "dna", $genome ) } elsif ( $format =~ /^blat$/i ) { warn "BLAT FORMAT NOT IMPLEMENTED" } elsif ( $format =~ /^vmatch$/i ) { Maasha::Match::vmatch_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/vmatch", $tmp_dir ) } - elsif ( $format =~ /^bowtie$/i ) { bowtie_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bowtie", $genome, $options->{ 'verbose' } ) } + elsif ( $format =~ /^bowtie$/i ) { Maasha::Bowtie::bowtie_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bowtie", $genome, $options->{ 'verbose' } ) } elsif ( $format =~ /^phastcons$/i ) { Maasha::UCSC::phastcons_index( "$genome.pp", $phastcons_dir ) } print STDERR qq(done.\n) if $options->{ 'verbose' }; @@ -127,31 +128,6 @@ Maasha::Biopieces::close_stream( $in ); Maasha::Biopieces::close_stream( $out ); -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -sub bowtie_index -{ - # Martin A. Hansen, July 2009. - - # Create a bowtie index for fast sequence mapping. - - my ( $src_file, # filename of source file - $dst_dir, # destination dir to store index - $base_name, # base name of index - $verbose, # verbose flag - ) = @_; - - Maasha::Filesys::dir_create_if_not_exists( $dst_dir ); - - if ( $verbose ) { - Maasha::Common::run( "bowtie-build", "$src_file $dst_dir/$base_name" ); - } else { - Maasha::Common::run( "bowtie-build", "$src_file $dst_dir/$base_name > /dev/null 2>&1" ); - } -} - - # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<