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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (13 years, 11 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 1.1: +17 -0 lines
Add license words.

# -*- perl -*-
#
# 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.
#


# usage: generate_sprout_links

use strict;
use FIG;
my $fig = new FIG;
use DBrtns;
my $dbf = $fig->db_handle;

my($org);

my $usage = "usage: generate_sprout_links GenomesFile > SproutData/FeatureLink";
my $genomesF;
(
 ($genomesF = shift @ARGV)
)
    || die $usage;

my %genomes = map { $_ =~ /^(\d+\.\d+)/; $1 => 1 } `cat $genomesF`;

foreach $org (sort { $a <=> $b } keys(%genomes))
{
    if ((-d "$FIG_Config::organisms/$org/Features") && opendir(TYPES,"$FIG_Config::organisms/$org/Features"))
    {
	my @types = grep { $_ !~ /^\./ } readdir(TYPES);
	closedir(TYPES);
	
	my $type;
	foreach $type (@types)
	{
	    if (opendir(FEAT,"$FIG_Config::organisms/$org/Features/$type"))
	    {
		my @links = grep { $_ =~ /links/ } readdir(FEAT);
		closedir(FEAT);
		
		my $file;
		foreach $file (@links)
		{
		    if (open(LINKS,"<$FIG_Config::organisms/$org/Features/$type/$file"))
		    {
			while (defined($_ = <LINKS>))
			{
			    chop;
			    my @flds = split(/\t/,$_);

			    if (@flds == 2)
			    {
				print "$_\n";
			    }
			    elsif (@flds == 3)
			    {
				my $link = join("",("<a href=",$flds[2],">",$flds[1],"</a>"));
				print "$flds[0]\t$link\n";
			    }
			}
			close(LINKS);
		    }
		}
	    }
	}
    }
}


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