adding bzip2 support in ruby

[biopieces.git] / bp_bin / transliterate_seq

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
deleted file mode 120000 (symlink)
index ce6ea54070788acd22e14d1d3f60a47e176ffc77..0000000000000000000000000000000000000000
--- a/bp_bin/transliterate_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/transliterate_seq
\ No newline at end of file

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..14dcb299f9ee0aecbd71af38fab9781119138941
--- /dev/null
+++ b/bp_bin/transliterate_seq
@@ -0,0 +1,92 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Transliterate chars from sequences in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $search, $replace, $delete );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'search',  short => 's', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'replace', short => 'r', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'delete',  short => 'd', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$search  = $options->{ "search" }  || "";
+$replace = $options->{ "replace" } || "";
+$delete  = $options->{ "delete" }  || "";
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "SEQ" } )
+    {
+        if ( $search and $replace ) {
+            eval "\$record->{ 'SEQ' } =~ tr/$search/$replace/";
+        } elsif ( $delete ) {
+            eval "\$record->{ 'SEQ' } =~ tr/$delete//d";
+
+            $record->{ "SEQ_LEN" } = length $record->{ "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__