migrated create_weight_matrix

git-svn-id: http://biopieces.googlecode.com/svn/trunk@416 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..44a211c2d180faaa1b0712c5feb6419f98c54777 100755 (executable)
--- 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 b9049f2398a3c76d86467dba3bdaf7f6c8ab234c..6fcb46e5e062efc1083fc212aabf079c6ed62714 100644 (file)
--- 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.