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Revision 1.1 - (download) (as text) (annotate)
Wed Nov 3 16:00:55 2010 UTC (9 years, 3 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_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2011_0119, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, 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_02222011, mgrast_dev_10262011, HEAD
New script to find intergenic regions.

use strict;
use Data::Dumper;
use Carp;

#
# This is a SAS Component
#


=head1 svr_intergenic_regions

List all the intergenic regions in the contigs for a specified genome.

Intergenic regions are defined here as areas of the contig not occupied by
features of specified types, usually PEG and/or RNA.

The genome ID and the types of features to be considered in computing the regions
are specified on the command line. The output will be a flat file containing
L<SAP/Location Strings>, one per line. For example,

    svr_intergenic_regions 360108.3 peg rna

would output strings for the locations in the contigs for genome 360108.3 that
are not used by PEGs or RNAs.

=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 just contains a location string.

=cut


use SeedEnv;
use Getopt::Long;

my $usage = "usage: svr_intergenic_regions Genome [Type1 Type2 ...]";

my $url;
my $opted =  GetOptions('url=s' => \$url);
if (! $opted) {
    print "$usage\n";
} else {
    my $genome = shift @ARGV or die $usage;
    my @types = @ARGV;

    my $sapObject = SAPserver->new(url => $url);
    
    my $locList = $sapObject->intergenic_regions(-genome => $genome,
                                                 -type => \@types);
    for my $loc (@$locList) {
        print "$loc\n";
    }
}

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