#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Locates and removes a specified adaptor sequence from sequences in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Common;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $adaptor, $seq, $adaptor_len,
+ $seq_len, $offset, $max_match, $max_mismatch, $pos );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'adaptor', short => 'a', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'mismatches', short => 'm', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'offset', short => 'o', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
+ { long => 'remove', short => 'r', type => 'string', mandatory => 'no', default => 'after', allowed => 'before,after,skip', disallowed => undef },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$max_mismatch = $options->{ "mismatches" };
+$offset = $options->{ "offset" };
+
+if ( not defined $offset ) {
+ $offset = 0;
+} else {
+ $offset--;
+}
+
+$adaptor = uc $options->{ "adaptor" };
+$adaptor_len = length $adaptor;
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $record->{ "SEQ" } )
+ {
+ $seq = uc $record->{ "SEQ" };
+ $seq_len = length $seq;
+
+ $pos = Maasha::Common::index_m( $seq, $adaptor, $seq_len, $adaptor_len, $offset, $max_mismatch );
+
+ $record->{ "ADAPTOR_POS" } = $pos;
+
+ if ( $pos >= 0 and $options->{ "remove" } ne "skip" )
+ {
+ if ( $options->{ "remove" } eq "after" )
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, 0, $pos;
+ $record->{ "SCORES" } = substr $record->{ "SCORES" }, 0, $pos if $record->{ "SCORES" };
+ $record->{ "SEQ_LEN" } = $pos;
+ }
+ else
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $pos + $adaptor_len;
+ $record->{ "SCORES" } = substr $record->{ "SCORES" }, $pos + $adaptor_len if $record->{ "SCORES" };
+ $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
+ }
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+ else
+ {
+ 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();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use Maasha::BioRun;
+__END__