#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read tabular data.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
use warnings;
use strict;
+use Data::Dumper;
+use Maasha::Filesys;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $data_in, $num, $skip, $line, @fields, @fields2, $i );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'delimit', short => 'd', type => 'string', mandatory => 'no', default => '\s+', allowed => undef, disallowed => undef },
+ { long => 'cols', short => 'c', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'skip', short => 's', type => 'uint', mandatory => 'no', default => '0', allowed => undef, disallowed => undef },
+ { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+ ]
+);
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( $options->{ 'data_in' } )
+{
+ $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
+
+ $num = 1;
+ $skip = $options->{ 'skip' };
+
+ while ( $line = <$data_in> )
+ {
+ chomp $line;
+
+ if ( $skip )
+ {
+ $skip--;
+ next;
+ }
+
+ next if $line =~ /^$/; # skip empty lines.
+
+ if ( $line =~ /^#.+/ and not defined $options->{ 'keys' } )
+ {
+ $line = substr $line, 1;
+
+ $options->{ 'keys' } = [ split /$options->{'delimit'}/, $line ];
+
+ next;
+ }
+
+ undef $record;
+ undef @fields2;
+
+ @fields = split /$options->{'delimit'}/, $line;
+
+ if ( $options->{ "cols" } ) {
+ map { push @fields2, $fields[ $_ ] } @{ $options->{ "cols" } };
+ } else {
+ @fields2 = @fields;
+ }
+
+ for ( $i = 0; $i < @fields2; $i++ )
+ {
+ if ( $options->{ "keys" }->[ $i ] ) {
+ $record->{ $options->{ "keys" }->[ $i ] } = $fields2[ $i ];
+ } else {
+ $record->{ "V" . $i } = $fields2[ $i ];
+ }
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+
+ last if $options->{ "num" } and $num == $options->{ "num" };
+
+ $num++;
+ }
+
+ close $data_in;
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use Maasha::Biotools;
+__END__