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Revision 1.1 - (download) (as text) (annotate)
Wed Jul 1 17:43:53 2009 UTC (10 years, 9 months ago) by olson
Branch: MAIN
add server-based call_genes

#!/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 FFserver;
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 genetic_code

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 $rc = GetOptions("genetic_code=i" => \$genetic_code,
                    "help" => \$help);

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

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

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

print $result;

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