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Revision 1.1 - (download) (as text) (annotate)
Tue Mar 23 18:44:06 2010 UTC (9 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, mgrast_dev_04082011, rast_rel_2010_0928, mgrast_dev_06072011, rast_rel_2010_0526, 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_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, rast_rel_2010_0827, myrast_33, mgrast_dev_04052011
Test program for ANNO server find-special-proteins.

### Test program for Ross's project.

use strict;
use SeedEnv;
use Tracer;
use Data::Dumper;
use gjoseqlib;
use find_special_proteins;

my $genome = $ARGV[0];
print "Reading contigs for $genome.\n";
my @contigs = gjoseqlib::read_fasta("$FIG_Config::organisms/$genome/contigs");
print "Connecting to server.\n";
my $anno = ANNOserver->new(url => 'http://bio-macpro-1.mcs.anl.gov/~parrello/FIG/anno_server.cgi');
print "Producing selenoprotein output.\n";
my $output = $anno->find_special_proteins({ -contigs => \@contigs });
my @list = @$output;
print "Producing pyrrolysine output.\n";
$output = $anno->find_special_proteins({ -contigs => \@contigs, -templates => 'pyrrolysine' });
push @list, @$output;
print "Results:\n" . Dumper(@list);

1;

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