From: martinahansen Date: Tue, 26 May 2009 12:12:21 +0000 (+0000) Subject: migrated create_vmatch_index X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=54a333024e8b424260bc82b9d706ea81d259d8f7;p=biopieces.git migrated create_vmatch_index git-svn-id: http://biopieces.googlecode.com/svn/trunk@417 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index index fdf5bd2..f956745 100755 --- a/bp_bin/create_vmatch_index +++ b/bp_bin/create_vmatch_index @@ -1,6 +1,105 @@ -#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Create a Vmatch index from sequences in stream for use with [vmatch_seq]. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Common; +use Maasha::Biopieces; +use Maasha::Filesys; +use Maasha::Seq; +use Maasha::Fasta; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $default, $formats, $options, $in, $out, $record, $file_tmp, $fh_tmp, $type, $entry ); + +$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 }, + { long => 'prefix_length', short => 'p', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +$file_tmp = $options->{ 'index_name' }; +$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 ); + + $type = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } ) if not defined $type; + } + + Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; +} + +close $fh_tmp; + +if ( $type eq "protein" ) { + Maasha::Common::run( "mkvtree", "-db $file_tmp -protein -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" ); +} else { + Maasha::Common::run( "mkvtree", "-db $file_tmp -dna -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" ); +} + +unlink $file_tmp; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +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 6fcb46e..d245f2b 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -146,7 +146,6 @@ sub run_script elsif ( $script eq "patscan_seq" ) { script_patscan_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 ) } elsif ( $script eq "write_bed" ) { script_write_bed( $in, $out, $options ) } elsif ( $script eq "write_psl" ) { script_write_psl( $in, $out, $options ) } elsif ( $script eq "write_fixedstep" ) { script_write_fixedstep( $in, $out, $options ) } @@ -422,14 +421,6 @@ sub get_options direction|d=s ); } - elsif ( $script eq "create_vmatch_index" ) - { - @options = qw( - index_name|i=s - prefix_length|p=s - no_stream|x - ); - } elsif ( $script eq "write_bed" ) { @options = qw( @@ -805,7 +796,6 @@ sub get_options } Maasha::Common::error( qq(no --database specified) ) if $script eq "remove_ucsc_tracks" and not $options{ "database" }; - 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|plot_phastcons_profiles|plot_karyogram/ and not $options{ "genome" }; @@ -2382,54 +2372,6 @@ sub script_match_seq } -sub script_create_vmatch_index -{ - # Martin A. Hansen, January 2008. - - # Create a vmatch index from sequences in the stream. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $record, $file_tmp, $fh_tmp, $type, $entry ); - - if ( $options->{ "index_name" } ) - { - $file_tmp = $options->{ 'index_name' }; - $fh_tmp = Maasha::Common::write_open( $file_tmp ); - } - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $options->{ "index_name" } and $entry = Maasha::Fasta::biopiece2fasta( $record ) ) - { - Maasha::Fasta::put_entry( $entry, $fh_tmp ); - - $type = Maasha::Seq::seq_guess_type( $entry->[ SEQ ] ) if not defined $type; - } - - Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; - } - - if ( $options->{ "index_name" } ) - { - close $fh_tmp; - - if ( $type eq "protein" ) { - Maasha::Common::run( "mkvtree", "-db $file_tmp -protein -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" ); - } else { - Maasha::Common::run( "mkvtree", "-db $file_tmp -dna -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" ); - } - - unlink $file_tmp; - } -} - - sub script_write_bed { # Martin A. Hansen, August 2007.