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Revision 1.2 - (download) (as text) (annotate)
Mon Oct 10 19:36:46 2011 UTC (8 years, 5 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2014_0912, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2014_0729, mgrast_release_3_1_2, mgrast_dev_10262011, HEAD
Changes since 1.1: +2 -0 lines
fix pod doc

#!/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 svr_call_rnas Script

=head2 Introduction

    svr_call_rnas [options]  genus species domain

Call RNAs using Annotation server.

This script takes a FASTA file of contigs from the standard input and writes
the result of finding RNAs using search_for_rnas to the stdout.

=head2 Command-Line Options

=over 4

=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($genus, $species, $domain);
my $help;
my $man;
my $url;

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

my $usage = [ "$0 [options] genus species domain <contigs.fasta >rnas.fasta",
	  "\t-help\tdisplay command-line options", ""];

if ($help)
    #pod2usage({-exitval => 1, -verbose => 2, -output => \*STDOUT});  
    print join "\n", @$usage;

if (@ARGV != 3)
    print STDERR join "\n", @$usage;

($genus, $species, $domain) = @ARGV;

# Create an ANNO server object.

my $ffServer = ANNOserver->new(url => $url);

# Pass the input file to the ANNO server to get assignments.
my $ret = $ffServer->find_rnas(-input => \*STDIN,
			       -genus => $genus,
			       -species => $species,
			       -domain => $domain);
my ($fa, $encoded_tbl)  = @$ret;

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

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