refactoring of assemble_pairs

[biopieces.git] / bp_bin / oligo_freq

diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
index c8c800fbc01100b8cd9e82c26358933e470ca42e..53029b661c1c70be8e64215c1ec98e49834a9129 100755 (executable)
--- a/bp_bin/oligo_freq
+++ b/bp_bin/oligo_freq
@@ -1,6 +1,97 @@
 #!/usr/bin/env perl
 
+# 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 ( $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;
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::Biotools;
+__END__