[Bio] / FigKernelScripts / peg_to_name.pl Repository:
ViewVC logotype

View of /FigKernelScripts/peg_to_name.pl

Parent Directory Parent Directory | Revision Log Revision Log

Revision 1.4 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (14 years, 2 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, caBIG-05Apr06-00, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, 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, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.3: +17 -0 lines
Add license words.

# 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.

# Filter, converts a sequence of PEGs, one per line, to
# the corresponding taxon and genus/species name.

use Getopt::Long;

my $show_fid = 1;
my $show_name = 1;
my $show_abbr= 0;
my $show_help = 0;
my $column = 1;
my $res = GetOptions("fid!" => \$show_fid,
		     "name!" => \$show_name,
		     "abbr!" => \$show_abbr,
		     "help" => \$show_help,
		     "column=i" => \$column,

if (!$res or $show_help)
    die "Usage: $0 [--nofid] [--noname] [--abbr] [--column n]\n";


use FIG;
$fig = new FIG();

while (<>)

    my @line = split;
    my @what;
    print join(":", @line), "\n";
    my $peg = $line[$column];
    if ($peg)
	my $genome = FIG::genome_of($peg);
	if ($genome)
	    my $org = $fig->org_of($peg);
	    my $gs = $fig->genus_species($genome);

	    push(@what, $genome) if $show_fid;
	    push(@what, &FIG::abbrev($org)) if $show_abbr;
	    push(@what, $org) if $show_name;
    splice(@line, $column, 1, @what);
    print join(" ", @line), "\n";

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3