removed debug message

[biopieces.git] / bp_bin / match_seq

diff --git a/bp_bin/match_seq b/bp_bin/match_seq
deleted file mode 120000 (symlink)
index 2843de1ba6458a630d558d59241dd21e610b4093..0000000000000000000000000000000000000000
--- a/bp_bin/match_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/match_seq
\ No newline at end of file

diff --git a/bp_bin/match_seq b/bp_bin/match_seq
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..d5362fa1a8f12dbd38dcc224aa8a50901c111260
--- /dev/null
+++ b/bp_bin/match_seq
@@ -0,0 +1,96 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Find all matches between sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::Match;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, @entries, $results, $tmp_dir );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'word_size', short => 'w', type => 'uint',   mandatory => 'no', default => 20,     allowed => undef,                  disallowed => 0 },
+        { long => 'direction', short => 'd', type => 'string', mandatory => 'no', default => 'both', allowed => 'both,forward,reverse', disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
+        push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+    }
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( @entries == 1 )
+{
+    $results = Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 0 ] ], $options, $tmp_dir );
+
+    map { Maasha::Biopieces::put_record( $_, $out ) } @{ $results };
+}
+else
+{
+    $results = Maasha::Match::match_mummer( [ shift @entries ], \@entries, $options, $tmp_dir );
+
+    map { Maasha::Biopieces::put_record( $_, $out ) } @{ $results };
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__