migrated oligo_freq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@432 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..7631103faac9544b07d88c8c1333f4448bea5f37 100755 (executable)
--- a/bp_bin/oligo_freq
+++ b/bp_bin/oligo_freq
@@ -1,6 +1,101 @@
-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Determines the oligo frequencies of sequences in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use warnings;
 use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @freq_table, %oligos );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'word_size', short => 'w', type => 'uint', mandatory => 'no', default => 7,     allowed => undef, disallowed => 0 },
+        { long => 'all',       short => 'a', 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" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "SEQ" } )
+    {
+        map { $oligos{ $_ }++ } Maasha::Seq::seq2oligos( \$record->{ "SEQ" }, $options->{ "word_size" } );
+
+        if ( not $options->{ "all" } )
+        {
+            @freq_table = Maasha::Seq::oligo_freq( \%oligos );
+
+            map { Maasha::Biopieces::put_record( $_, $out ) } @freq_table;
+        
+            undef %oligos;
+        }
+    }
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( defined $options->{ "all" } )
+{
+    @freq_table = Maasha::Seq::oligo_freq( \%oligos );
+
+    map { Maasha::Biopieces::put_record( $_, $out ) } @freq_table;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 2c26f6390fe37d29d769bfdcad871b55f3ac2212..1f2ffeb3ad4e1b895eb44964f10a414cf9943397 100644 (file)
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -132,7 +132,6 @@ sub run_script
     elsif ( $script eq "read_ucsc_config" )         { script_read_ucsc_config(          $in, $out, $options ) }
     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 "remove_indels" )            { script_remove_indels(             $in, $out, $options ) }
     elsif ( $script eq "get_genome_align" )         { script_get_genome_align(          $in, $out, $options ) }
     elsif ( $script eq "get_genome_phastcons" )     { script_get_genome_phastcons(      $in, $out, $options ) }
@@ -304,13 +303,6 @@ sub get_options
             num|n=s
         );
     }
-    elsif ( $script eq "oligo_freq" )
-    {
-        @options = qw(
-            word_size|w=s
-            all|a
-        );
-    }
     elsif ( $script eq "get_genome_align" )
     {
         @options = qw(
@@ -1536,51 +1528,6 @@ sub script_complexity_seq
 }
 
 
-sub script_oligo_freq
-{
-    # Martin A. Hansen, August 2007.
-
-    # Determine the length of sequences in stream.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $record, %oligos, @freq_table );
-
-    $options->{ "word_size" } ||= 7;
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-    {
-        if ( $record->{ "SEQ" } )
-        {
-            map { $oligos{ $_ }++ } Maasha::Seq::seq2oligos( \$record->{ "SEQ" }, $options->{ "word_size" } );
-
-            if ( not $options->{ "all" } )
-            {
-                @freq_table = Maasha::Seq::oligo_freq( \%oligos );
-
-                map { Maasha::Biopieces::put_record( $_, $out ) } @freq_table;
-            
-                undef %oligos;
-            }
-        }
-
-        Maasha::Biopieces::put_record( $record, $out );
-    }
-
-    if ( $options->{ "all" } )
-    {
-        @freq_table = Maasha::Seq::oligo_freq( \%oligos );
-
-        map { Maasha::Biopieces::put_record( $_, $out ) } @freq_table;
-    }
-}
-
-
 sub script_remove_indels
 {
     # Martin A. Hansen, August 2007.