From f26e561ce68e6f3b870b760bd388cae9eb3fdbd7 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Tue, 8 Sep 2009 07:09:04 +0000 Subject: [PATCH] fuckup git-svn-id: http://biopieces.googlecode.com/svn/trunk@660 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/create_bwa_index | 104 +++++++++++++++++++++++++++++++++++++ code_perl/Maasha/Bowtie.pm | 69 ------------------------ 2 files changed, 104 insertions(+), 69 deletions(-) create mode 100755 bp_bin/create_bwa_index delete mode 100644 code_perl/Maasha/Bowtie.pm diff --git a/bp_bin/create_bwa_index b/bp_bin/create_bwa_index new file mode 100755 index 0000000..9ccb0e4 --- /dev/null +++ b/bp_bin/create_bwa_index @@ -0,0 +1,104 @@ +#!/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 BWA index from sequences in stream for use with [bwa_seq]. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +use warnings; +use strict; +use Maasha::Common; +use Maasha::Biopieces; +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 => 'directory', short => 'd', type => 'dir', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + ] +); + +Maasha::Common::error( qq(Directory already exists: "$options->{ 'directory' }") ) if -d $options->{ 'directory' }; + +Maasha::Filesys::dir_create_if_not_exists( $options->{ 'directory' } ); + +$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_bwa_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::Filesys::dir_create_if_not_exists( $options->{ 'directory' } ); + +if ( $options->{ 'verbose' } ) { + Maasha::Common::run( "bwa", "index -p $options->{ 'directory' }/$options->{ 'index_name' } $file_tmp" ); +} else { + Maasha::Common::run( "bwa", "index -p $options->{ 'directory' }/$options->{ 'index_name' } $file_tmp > /dev/null 2>&1" ); +} + +unlink $file_tmp; + +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/Bowtie.pm b/code_perl/Maasha/Bowtie.pm deleted file mode 100644 index fce2fbf..0000000 --- a/code_perl/Maasha/Bowtie.pm +++ /dev/null @@ -1,69 +0,0 @@ -package Maasha::Bowtie; - -# Copyright (C) 2006-2009 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -# Routines for manipulation of bowtie indexes and results. - -# http://bowtie-bio.sourceforge.net/index.shtml - - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -use warnings; -use strict; -use Data::Dumper; -use vars qw( @ISA @EXPORT ); - -@ISA = qw( Exporter ); - - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -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" ); - } -} - - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -1; -- 2.39.5