rewrite begin

[biopieces.git] / bp_bin / extract_seq

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..bdd8104bf5855e6c0ff6f0bfd55af7b034cd146e 100755 (executable)
--- a/bp_bin/extract_seq
+++ b/bp_bin/extract_seq
@@ -1,6 +1,98 @@
-#!/usr/bin/env perl
+#!/usr/bin/env perl -w
+
+# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Split the values of a key into new key/value pairs.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use warnings;
 use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @vals, $i );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'key',     short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'keys',    short => 'K', type => 'list',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'delimit', short => 'd', type => 'string', mandatory => 'no',  default => '_',   allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+    if ( exists $options->{ 'key' } and exists $record->{ $options->{ 'key' } } )
+    {
+        @vals = split /$options->{ 'delimit' }/, $record->{ $options->{ 'key' } };
+
+        if ( scalar @vals > 1 )
+        {
+            for ( $i = 0; $i < @vals; $i++ )
+            {
+                if ( defined $options->{ "keys" } and defined $options->{ "keys" }->[ $i ] ) {
+                    $record->{ $options->{ "keys" }->[ $i ] } = $vals[ $i ];
+                } else {
+                    $record->{ $options->{ 'key' } . "_$i" } = $vals[ $i ];
+                }
+            }
+        }
+    }
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    $run_time_beg = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::log_biopiece();
+}
+
+
+END
+{
+    Maasha::Biopieces::close_stream( $in );
+    Maasha::Biopieces::close_stream( $out );
+
+    $run_time_end = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
 
-use Maasha::BioRun;