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Revision 1.4 - (download) (as text) (annotate)
Thu Dec 17 21:38:54 2009 UTC (10 years, 3 months ago) by olson
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_2010_0118, 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 1.3: +1 -1 lines
fix ANNOserver args

#!/usr/bin/perl -w

# This is a SAS Component

# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
# This file is part of the SEED Toolkit.
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License.
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.

use strict;
use ANNOserver;
use Getopt::Long;
#use Pod::Usage;

=head1 call_genes Script

=head2 Introduction

    call_genes [options] 

Call Genes using FF server.

This script takes a FASTA file of contigs from the standard input and writes
the result of calling genes using Glimmer to the standard output.

=head2 Command-Line Options

=over 4

=item --geneticCode

A number, generally either 11 or 4, representing the genetic code of the
given contigs.

=item help

Display this command's parameters and options.

=head3 Output Format

The standard output is FASTA file of proteins.


# Get the command-line options and parameters.
my $genetic_code = 11;
my $help;
my $man;
my $url;

my $rc = GetOptions("geneticCode=i" => \$genetic_code,
		    "url=s" => \$url,
                    "help" => \$help);

if ($help)
    #pod2usage({-exitval => 1, -verbose => 2, -output => \*STDOUT});  
    my $usage = [ "$0 [options]",
		  "\t-geneticCode\tgenetic code for this organism (default 11)",
		  "\t-help\tdisplay command-line options", ""];
    print join "\n", @$usage;

# Create a FIGfam server object.
my $ffServer = ANNOserver->new(url => $url);

# Pass the input file to the FIGfam server to get assignments.
my $ret = $ffServer->call_genes(-input => \*STDIN,
				-geneticCode => $genetic_code);
my ($fa, $encoded_tbl)  = @$ret;

print $fa;
print STDERR join("\t", @$_), "\n" for @$encoded_tbl;

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