added uniq_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@859 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/uniq_seq b/bp_bin/uniq_seq
new file mode 100755 (executable)
index 0000000..a261875
--- /dev/null
+++ b/bp_bin/uniq_seq
@@ -0,0 +1,115 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Count sequences from the stream and select only unique sequences.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Common;
+use Maasha::Biopieces;
+use Maasha::Seq;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, %hash, $record, $seq, $rc_seq, $type );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'complement', short => 'c', 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' } ) {
+        $hash{ $record->{ 'SEQ' } }++;
+    } else {
+        Maasha::Biopieces::put_record( $record, $out );
+    }
+}
+
+if ( $options->{ 'complement' } )
+{
+    foreach $seq ( keys %hash )
+    {
+        $type = Maasha::Seq::seq_guess_type( $seq ) if not $type;
+
+        if ( $type eq 'DNA' ) {
+            $rc_seq = Maasha::Seq::dna_revcomp( $seq );
+        } elsif ( $type eq 'RNA' ) {
+            $rc_seq = Maasha::Seq::rna_revcomp( $seq );
+        } else {
+            Maasha::Common::error( "Cannot reverse-complement protein sequence" );
+        }
+
+        if ( exists $hash{ $rc_seq } )
+        {
+            $hash{ $seq } += $hash{ $rc_seq };
+
+            delete $hash{ $rc_seq };
+        }
+    }
+}
+
+foreach $seq ( keys %hash )
+{
+    $record = {
+        SEQ       => $seq,
+        SEQ_LEN   => length $seq,
+        SEQ_COUNT => $hash{ $seq },
+    };
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__