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Revision 1.3 - (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 1.2: +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.
#


use FIG;
my $fig = new FIG;

use tree_utilities;

# usage: paint_tree [AttrFile] [newick=NewickTree]

$attrs = undef;
$newick = undef;

foreach $arg (@ARGV)
{
    if ($arg =~ /^newick=(\S+)/)
    {
	$newick = $1;
    }
    else
    {
	$attrs = $arg;
    }
}


my %to_paint;
if ($attrs)
{
    foreach $_ (`cat $attrs`)
    {
	if ($_ =~ /^(\S+)\t(\S.*\S)/)
	{
	    $to_paint{$1} = $2;
	}
    }
}

if ($newick)
{
    if ($tree = &parse_newick_tree(join("",`cat $newick`)))
    {
	$ids = &tips_of_tree($tree);
    }
}
else
{
    ($tree,$ids) = &build_tree_of_complete;
}

if (! $tree)
{
    print STDERR "Sorry, but the tree could not be accessed\n";
    exit;
}

$relabel = {};
foreach $id (@$ids)
{
    if ($gs = $fig->genus_species($id))
    {
	if ($extra = $to_paint{$id})
	{
	    $relabel->{$id} = "$extra: $gs ($id)";
	}
	else
	{
	    $relabel->{$id} = "$gs ($id)";
	}
    }
}
#&print_tree($tree);
$_ = &display_tree($tree,$relabel);
print "$_\n";

sub build_tree_of_complete {
    my(@last,@tax,$i,$prefix,$lev);

    open(TMP,">/tmp/tree$$") || die "could not open /tmp/tree$$";
    print TMP "1. root\n";

    @last = ();

    
    foreach $genome ($fig->sort_genomes_by_taxonomy($fig->genomes("complete")))
    {
	$tax = $fig->taxonomy_of($genome);
	@tax = split(/\s*;\s*/,$tax);
	push(@tax,$genome);
	for ($i=0; ((@last > $i) && (@tax > $i) && ($last[$i] eq $tax[$i])); $i++) {}
	while ($i < @tax)
	{
	    $lev = $i+2;
	    $prefix = " " x (4 * ($lev-1));
	    print TMP "$prefix$lev\. $tax[$i]\n";
	    $i++;
	}
	@last = @tax;
    }
    close(TMP);
    my $tree = &build_tree_from_outline("/tmp/tree$$");

    unlink("/tmp/tree$$");
    return ($tree,&tips_of_tree($tree));
}

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