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1 : parrello 1.1 ### Test program for Ross's project.
2 :    
3 :     use strict;
4 :     use SeedEnv;
5 :     use Tracer;
6 :     use Data::Dumper;
7 :     use gjoseqlib;
8 :     use find_special_proteins;
9 :    
10 :     my $genome = $ARGV[0];
11 :     print "Reading contigs for $genome.\n";
12 :     my @contigs = gjoseqlib::read_fasta("$FIG_Config::organisms/$genome/contigs");
13 :     print "Connecting to server.\n";
14 :     my $anno = ANNOserver->new(url => 'http://bio-macpro-1.mcs.anl.gov/~parrello/FIG/anno_server.cgi');
15 :     print "Producing selenoprotein output.\n";
16 :     my $output = $anno->find_special_proteins({ -contigs => \@contigs });
17 :     my @list = @$output;
18 :     print "Producing pyrrolysine output.\n";
19 :     $output = $anno->find_special_proteins({ -contigs => \@contigs, -templates => 'pyrrolysine' });
20 :     push @list, @$output;
21 :     print "Results:\n" . Dumper(@list);
22 :    
23 :     1;

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