-#!/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__
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 ) }
all|a
);
}
- elsif ( $script eq "create_weight_matrix" )
- {
- @options = qw(
- percent|p
- );
- }
elsif ( $script eq "transliterate_seq" )
{
@options = qw(
}
-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.