-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
# Copyright (C) 2007-2009 Martin A. Hansen.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
use Maasha::Biopieces;
+use Maasha::Calc;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $options, $in, $out, $record, $key, $fh, %min_hash, $min_record );
+my ( $options, $in, $out, $record, $new_record, $key, $fh, %min_hash );
$options = Maasha::Biopieces::parse_options(
[
- { 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 => 'keys', short => 'k', type => 'list', mandatory => 'yes', default => undef, 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 => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'list', short => 'l', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
]
);
+Maasha::Common::error( qq(both --keys and --list specified) ) if $options->{ "keys" } and $options->{ "list" };
+Maasha::Common::error( qq(no --keys or --list specified) ) if not $options->{ "keys" } and not $options->{ "list" };
+
$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
}
}
+ if ( $options->{ 'list' } and $record->{ $options->{ 'list' } } ) {
+ $record->{ $options->{ 'list' } . "_MIN" } = sprintf( "%.2f", Maasha::Calc::list_min( [ split ";", $record->{ $options->{ 'list' } } ] ) );
+ }
+
Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
}
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
-foreach $key ( @{ $options->{ "keys" } } )
-{
- $min_record->{ $key . "_MIN" } = $min_hash{ $key };
+foreach $key ( @{ $options->{ "keys" } } ) {
+ $new_record->{ $key . "_MIN" } = $min_hash{ $key };
}
-Maasha::Biopieces::put_record( $min_record, $fh );
+if ( $options->{ "keys" } and $new_record )
+{
+ $new_record->{ 'REC_TYPE' } = "MIN";
-close $fh;
+ Maasha::Biopieces::put_record( $new_record, $fh );
+}
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
+close $fh;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<