migrated calc_bit_scores

git-svn-id: http://biopieces.googlecode.com/svn/trunk@408 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..9e98c2ec48ef8bf9d0aeb9cf6aa6a89fe82b15d1 100755 (executable)
--- 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 ef4891143ec31f9e428b05c965a8fd8b7371f61d..edb52b027f7640ee632fb6ffce8a4f33e7c766e4 100644 (file)
--- 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.