removed debug message

[biopieces.git] / bp_bin / write_fixedstep

diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..17957c1bd978eb34b5b247202f7387b388084374 100755 (executable)
--- a/bp_bin/write_fixedstep
+++ b/bp_bin/write_fixedstep
@@ -1,6 +1,89 @@
 #!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Write fixedStep from records in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::UCSC::Wiggle;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $fh, $record, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'key',       short => 'k', type => 'string', mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'step',      short => 's', type => 'uint',   mandatory => 'no',  default => 1,     allowed => undef, disallowed => undef },
+        { long => 'no_stream', short => 'x', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'data_out',  short => 'o', type => 'file',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'compress',  short => 'Z', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $entry = Maasha::UCSC::Wiggle::biopiece2fixedstep( $record, $options->{ "key" }, $options->{ "step" } ) ) {
+        Maasha::UCSC::Wiggle::fixedstep_entry_put( $entry, $fh );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+close $fh;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::BioRun;
+__END__