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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (14 years, 3 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.

#
# 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: compare_tree_and_alignment Alignment Tree IdsInOnlyTree IdsInOnlyAli InBoth

use tree_utilities;

$usage = "usage: compare_tree_and_alignment Alignment Tree IdsInOnlyTree IdsInOnlyAli InBoth";
($ali = shift @ARGV) 
    || die "bad alignment: $usage";

($tree_file = shift @ARGV)
    || die "missing tree: $usage";

($tree_only = shift @ARGV)
    || die "missing tree_only: $usage";

($ali_only = shift @ARGV)
    || die "missing ali_only: $usage";

($in_both = shift @ARGV)
    || die "missing in_both: $usage";

open(TONLY,">$tree_only") || die "could not open $tree_only";
open(AONLY,">$ali_only")  || die "could not open $ali_only";
open(BOTH,">$in_both")    || die "could not open $in_both";

@ali = `grep \">\" $ali`;
foreach $x (@ali)
{
    if ($x =~ /^>(\S+)/)
    {
	$x = $1;
	$ali{$x} = 1;
    }
}

($tree = &parse_newick_tree(join("",`cat \"$tree_file\"`)))
    || die "could not parse the tree";

$tips = &tips_of_tree($tree);
foreach $x (@$tips)
{
    $y = &label_to_printable($x);
    $tree{$y} = 1;
}

foreach $x (sort keys(%tree))
{
    if ($ali{$x})
    {
	print BOTH "$x\n";
    }
    else
    {
	print TONLY "$x\n";
    }
}

foreach $x (sort keys(%ali))
{
    if (! $tree{$x})
    {
	print AONLY "$x\n";
    }
}
close(AONLY);
close(TONLY);
close(BOTH);


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