removed debug message

[biopieces.git] / bp_bin / fold_seq

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
deleted file mode 120000 (symlink)
index c5f37283ab5c09e4801ef6249850dc5c322dc5da..0000000000000000000000000000000000000000
--- a/bp_bin/fold_seq
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/fold_seq
\ No newline at end of file

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..4543920c2f749484ac3dddcd7311a677075780d4
--- /dev/null
+++ b/bp_bin/fold_seq
@@ -0,0 +1,86 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Fold sequences in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $type, $struct, $index );
+
+$options = Maasha::Biopieces::parse_options();
+
+$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" } )
+    {
+        $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } ) if not $type;
+        
+        if ( $type ne "PROTEIN" )
+        {
+            ( $struct, $index ) = Maasha::Seq::fold_struct_rnafold( $record->{ "SEQ" } );
+            $record->{ "SEC_STRUCT" }  = $struct;
+            $record->{ "FREE_ENERGY" } = $index;
+            $record->{ "SCORE" }       = abs int $index;
+            $record->{ "SIZE" }        = length $struct;
+            $record->{ "CONF" }        = "1," x $record->{ "SIZE" };
+        }
+    }
+
+    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__