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Revision 1.1 - (download) (as text) (annotate)
Thu Mar 17 18:51:58 2011 UTC (8 years, 8 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2014_0729, mgrast_dev_03252011, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_10262011, HEAD
New script to list expression-data genomes.

use strict;

use Getopt::Long;
use SeedUtils;
use SAPserver;

#
# This is a SAS Component
#


=head1 svr_exp_genomes

List the names and IDs of all the genomes with expression data.

There is no input.  The output is a file of genome names and genome IDs.

------
Example: svr_exp_genomes > expression_data_genomes.tbl

would produce a 2-column table.  The first column would contain the
names of all complete genomes, and the second the IDs of those genomes.
------

=head2 Command-Line Options

=over 4

=item url

The URL for the Sapling server, if it is to be different from the default.

=back

=head2 Output Format

The standard output is a file where each line contains a genome name and a genome ID.

=cut

my $usage    = "usage: svr_exp_genomes [--url=http://...] >output\n";
my $complete = 0;
my $url = '';
my $opted    = GetOptions('complete' => \$complete, 'url=s', \$url);

if (! $opted) {
    print $usage;
} else {
    my $sapObject  = SAPserver->new(url => $url);
    my $genomeHash = $sapObject->expressed_genomes( -names => 1 );
    while (my ($id, $name) = each %$genomeHash ) {
        print "$name\t$id\n";
    }
}

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