From 03a0cab1a403d0f9af77127cb5133ccb1b7c9f45 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Mon, 25 May 2009 12:22:22 +0000 Subject: [PATCH] migrated calc_bit_scores git-svn-id: http://biopieces.googlecode.com/svn/trunk@408 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/calc_bit_scores | 115 ++++++++++++++++++++++++++++++++++++- code_perl/Maasha/BioRun.pm | 61 -------------------- 2 files changed, 112 insertions(+), 64 deletions(-) diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores index fdf5bd2..9e98c2e 100755 --- a/bp_bin/calc_bit_scores +++ b/bp_bin/calc_bit_scores @@ -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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Calculate the bit score for each position based on an alignment in the stream. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Seq; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $count, $i, $res, $type, $bit_max, %freq_hash, $bit_height, $bit_diff ); + +$options = Maasha::Biopieces::parse_options(); + +$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" } ) + { + $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type; + + for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ ) + { + $res = substr $record->{ "SEQ" }, $i, 1; + + next if $res =~ /-|_|~|\./; + + $freq_hash{ $i }{ $res }++; + } + + $count++; + } + else + { + Maasha::Biopieces::put_record( $record, $out ); + } +} + +undef $record; + +if ( $type eq "protein" ) { + $bit_max = 4; +} else { + $bit_max = 2; +} + +for ( $i = 0; $i < keys %freq_hash; $i++ ) +{ + $bit_height = Maasha::Seq::seqlogo_calc_bit_height( $freq_hash{ $i }, $count ); + + $bit_diff = $bit_max - $bit_height; + + $record->{ "V" . ( $i ) } = sprintf( "%.2f", $bit_diff ); +} + +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 ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ + -use Maasha::BioRun; diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index ef48911..edb52b0 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -135,7 +135,6 @@ sub run_script 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 "calc_bit_scores" ) { script_calc_bit_scores( $in, $out, $options ) } elsif ( $script eq "calc_fixedstep" ) { script_calc_fixedstep( $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 ) } @@ -1834,66 +1833,6 @@ sub script_create_weight_matrix } -sub script_calc_bit_scores -{ - # Martin A. Hansen, March 2007. - - # Calculates the bit scores for each position from an alignmnet in the stream. - - my ( $in, # handle to in stream - $out, # handle to out stream - ) = @_; - - # Returns nothing. - - my ( $record, $type, $count, $i, $res, %freq_hash, $bit_max, $bit_height, $bit_diff ); - - $count = 0; - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $record->{ "SEQ" } ) - { - $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type; - - for ( $i = 0; $i < length $record->{ "SEQ" }; $i++ ) - { - $res = substr $record->{ "SEQ" }, $i, 1; - - next if $res =~ /-|_|~|\./; - - $freq_hash{ $i }{ $res }++; - } - - $count++; - } - else - { - Maasha::Biopieces::put_record( $record, $out ); - } - } - - undef $record; - - if ( $type eq "protein" ) { - $bit_max = 4; - } else { - $bit_max = 2; - } - - for ( $i = 0; $i < keys %freq_hash; $i++ ) - { - $bit_height = Maasha::Seq::seqlogo_calc_bit_height( $freq_hash{ $i }, $count ); - - $bit_diff = $bit_max - $bit_height; - - $record->{ "V" . ( $i ) } = sprintf( "%.2f", $bit_diff ); - } - - Maasha::Biopieces::put_record( $record, $out ); -} - - sub script_calc_fixedstep { # Martin A. Hansen, September 2008. -- 2.39.2