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Revision 1.3 - (download) (as text) (annotate)
Wed Mar 31 19:04:31 2010 UTC (10 years 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_2010_0526, 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 1.2: +6 -4 lines
Fixed for server paper.

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

use ANNOserver;
use Data::Dumper;

# Reads FASTA protein sequences from STDIN. 
# Produces sequence ID, role, genome set name, confidence
# If "-blast" is specified, uses BLAST option.

my $annoObject = ANNOserver->new();
my $blastOption = ($ARGV[0] && $ARGV[0] =~ /^-blast/i ? 1 : 0);

my $results = $annoObject->assign_function_to_prot(-input => \*STDIN,
                                                   -kmer => 8,
                                                   -scoreThreshold => 3,
                                                   -assignToAll => $blastOption);
while (my $data = $results->get_next()) {
    my ($id, $role, $genomeSet, undef, $hits) = @$data;
    # Only proceed if a role was found.
    if ($role) {
        $genomeSet = '' if ! defined $genomeSet;
        print join("\t", $id, $role, $genomeSet, $hits) . "\n";
    }
}

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