From 722826f02edcb5ceda1ec5c0fda3e08b99d6a4d6 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Sun, 24 May 2009 10:35:56 +0000 Subject: [PATCH] migrated write_align git-svn-id: http://biopieces.googlecode.com/svn/trunk@394 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/write_align | 96 ++++++++++++++++++++++++++++++++++++-- code_perl/Maasha/BioRun.pm | 47 ------------------- 2 files changed, 93 insertions(+), 50 deletions(-) diff --git a/bp_bin/write_align b/bp_bin/write_align index fdf5bd2..dcbe345 100755 --- a/bp_bin/write_align +++ b/bp_bin/write_align @@ -1,6 +1,96 @@ -#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Write aligned sequences from the stream as a pretty alignment. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Align; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_out, @entries ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'wrap', short => 'w', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' }, + { long => 'no_ruler', short => 'R', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'no_consensus', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +$data_out = Maasha::Biopieces::write_stream( $options->{ "data_out" } ) ; + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) { + push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ]; + } + + Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; +} + +if ( scalar( @entries ) == 2 ) { + Maasha::Align::align_print_pairwise( $entries[ 0 ], $entries[ 1 ], $data_out, $options->{ "wrap" } ); +} elsif ( scalar ( @entries ) > 2 ) { + Maasha::Align::align_print_multi( \@entries, $data_out, $options->{ "wrap" }, $options->{ "no_ruler" }, $options->{ "no_consensus" } ); +} + +close $data_out; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +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 ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use Maasha::BioRun; +__END__ diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index c54c9ef..e5845d3 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -156,7 +156,6 @@ sub run_script 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_align" ) { script_write_align( $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 ) } @@ -490,16 +489,6 @@ sub get_options no_stream|x ); } - elsif ( $script eq "write_align" ) - { - @options = qw( - wrap|w=s - no_stream|x - no_ruler|R - no_consensus|C - data_out|o=s - ); - } elsif ( $script eq "write_bed" ) { @options = qw( @@ -3011,42 +3000,6 @@ sub script_create_vmatch_index } -sub script_write_align -{ - # Martin A. Hansen, August 2007. - - # Write pretty alignments aligned sequences in stream. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $fh, $record, @entries ); - - $fh = write_stream( $options->{ "data_out" } ) ; - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) { - push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ]; - } - - Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; - } - - if ( scalar( @entries ) == 2 ) { - Maasha::Align::align_print_pairwise( $entries[ 0 ], $entries[ 1 ], $fh, $options->{ "wrap" } ); - } elsif ( scalar ( @entries ) > 2 ) { - Maasha::Align::align_print_multi( \@entries, $fh, $options->{ "wrap" }, $options->{ "no_ruler" }, $options->{ "no_consensus" } ); - } - - close $fh if $fh; -} - - sub script_write_bed { # Martin A. Hansen, August 2007. -- 2.39.5