From feaa3fbccdc23c3bf35c5a9861cede0f69a6b62f Mon Sep 17 00:00:00 2001 From: martinahansen Date: Tue, 26 May 2009 11:26:04 +0000 Subject: [PATCH] migrated create_weight_matrix git-svn-id: http://biopieces.googlecode.com/svn/trunk@416 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/create_weight_matrix | 115 +++++++++++++++++++++++++++++++++++- code_perl/Maasha/BioRun.pm | 66 --------------------- 2 files changed, 112 insertions(+), 69 deletions(-) diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix index fdf5bd2..44a211c 100755 --- a/bp_bin/create_weight_matrix +++ b/bp_bin/create_weight_matrix @@ -1,6 +1,115 @@ -#!/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 residue composition weight matrix of an alignment in the stream. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Common; +use Maasha::Biopieces; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $count, $i, $res, %freq_hash, %res_hash, $freq ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'percent', short => 'p', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +$count = 0; + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + if ( $record->{ "SEQ" } ) + { + for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ ) + { + $res = substr $record->{ "SEQ" }, $i, 1; + + $freq_hash{ $i }{ $res }++; + $res_hash{ $res } = 1; + } + + $count++; + } + else + { + Maasha::Biopieces::put_record( $record, $out ); + } +} + +foreach $res ( sort keys %res_hash ) +{ + undef $record; + + $record->{ "V0" } = $res; + + for ( $i = 0; $i < keys %freq_hash; $i++ ) + { + $freq = $freq_hash{ $i }{ $res } || 0; + + if ( $options->{ "percent" } ) { + $freq = sprintf( "%.0f", 100 * $freq / $count ) if $freq > 0; + } + + $record->{ "V" . ( $i + 1 ) } = $freq; + } + + Maasha::Biopieces::put_record( $record, $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 b9049f2..6fcb46e 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -134,7 +134,6 @@ sub run_script elsif ( $script eq "uppercase_seq" ) { script_uppercase_seq( $in, $out, $options ) } elsif ( $script eq "complexity_seq" ) { script_complexity_seq( $in, $out, $options ) } elsif ( $script eq "oligo_freq" ) { script_oligo_freq( $in, $out, $options ) } - elsif ( $script eq "create_weight_matrix" ) { script_create_weight_matrix( $in, $out, $options ) } elsif ( $script eq "remove_indels" ) { script_remove_indels( $in, $out, $options ) } elsif ( $script eq "transliterate_seq" ) { script_transliterate_seq( $in, $out, $options ) } elsif ( $script eq "transliterate_vals" ) { script_transliterate_vals( $in, $out, $options ) } @@ -336,12 +335,6 @@ sub get_options all|a ); } - elsif ( $script eq "create_weight_matrix" ) - { - @options = qw( - percent|p - ); - } elsif ( $script eq "transliterate_seq" ) { @options = qw( @@ -1745,65 +1738,6 @@ sub script_oligo_freq } -sub script_create_weight_matrix -{ - # Martin A. Hansen, August 2007. - - # Creates a weight matrix from an alignmnet. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $record, $count, $i, $res, %freq_hash, %res_hash, $freq ); - - $count = 0; - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $record->{ "SEQ" } ) - { - for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ ) - { - $res = substr $record->{ "SEQ" }, $i, 1; - - $freq_hash{ $i }{ $res }++; - $res_hash{ $res } = 1; - } - - $count++; - } - else - { - Maasha::Biopieces::put_record( $record, $out ); - } - } - - foreach $res ( sort keys %res_hash ) - { - undef $record; - - $record->{ "V0" } = $res; - - for ( $i = 0; $i < keys %freq_hash; $i++ ) - { - $freq = $freq_hash{ $i }{ $res } || 0; - - if ( $options->{ "percent" } ) { - $freq = sprintf( "%.0f", 100 * $freq / $count ) if $freq > 0; - } - - $record->{ "V" . ( $i + 1 ) } = $freq; - } - - Maasha::Biopieces::put_record( $record, $out ); - } -} - - sub script_remove_indels { # Martin A. Hansen, August 2007. -- 2.39.2