[Bio] / FigKernelScripts / svr_all_figfams.pl Repository:
ViewVC logotype

View of /FigKernelScripts/svr_all_figfams.pl

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (download) (as text) (annotate)
Tue May 18 19:38:33 2010 UTC (9 years, 6 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, rast_rel_2010_0928, 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, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
Changes since 1.1: +1 -1 lines
Documentation fixes.

#!/usr/bin/perl -w
use strict;

use Getopt::Long;
use SAPserver;
use ScriptThing;

#
#	This is a SAS Component.
#

=head1 svr_all_figfams

    svr_all_figfams >figfam_data.tbl

List all the features in each FIGfam.

This is a very simple script that loops through all the FIGfams locating the features
in each. For each feature found, it will output a line containing the FIGfam ID followed
by the feature ID with an intervening tab.

The output will be large, since every feature in a FIGfam will be listed. A feature
that is in more than one FIGfam (if one exists) will appear once for each FIGfam.

=head2 Command-Line Options

=over 4

=item url

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

=back

=cut

# Parse the command-line options.
my $url = '';
my $opted =  GetOptions('url=s' => \$url);
if (! $opted) {
    print "usage: svr_all_figfams [--url=http://...] >output\n";
} else {
    # Get the server object.
    my $sapObject = SAPserver->new(url => $url);
    # Get the complete list of FIGfams.
    my $ffHash = $sapObject->all_figfams();
    # Loop through them in lexical order.
    for my $figfam (sort keys %$ffHash) {
        # Get all the features in this FIGfam.
        my $fidList = $sapObject->figfam_fids(-id => $figfam);
        # Loop through the features, writing them to the output.
        for my $fid (@$fidList) {
            print "$figfam\t$fid\n";
        }
    }
}


MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3