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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:38 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.

#
# 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.
#


my $usage = "usage: report_changes Replacements Deletions OldData NewData";

(
 ($repF = shift @ARGV) &&
 ($delF = shift @ARGV) &&
 ($oldD = shift @ARGV) &&
 ($newD = shift @ARGV)
)
    || die $usage;

foreach $_ (`cat $repF`)
{
    if ($_ =~ /^(\d+\.\d+)\t(\d+\.\d+)$/)
    {
	$rep{$1} = $2;
	$a_replacement{$2} = $1;
    }
    else
    {
	print STDERR "bad map: $_";
    }
}

foreach $_ (`cat $delF`)
{
    if ($_ =~ /^(\d+\.\d+)$/)
    {
	$del{$1} = 1;
    }
    else
    {
	print STDERR "bad delete: $_";
    }
}

opendir(OLD,"$oldD/Organisms") || die "could not get at $oldD/Organisms";
my @old = grep { $_ !~ /^\./ } readdir(OLD);
closedir(OLD);

opendir(NEW,"$newD/Organisms") || die "could not get at $newD/Organisms";
my @new = grep { $_ !~ /^\./ } readdir(NEW);
closedir(NEW);

my %old = map { $_ => 1 } @old;
my %new = map { $_ => 1 } @new;

foreach $_ (@old)
{
    if ((! $new{$_}) && (! $del{$_}))
    {
	print STDERR "BAD ERROR: Lost $_\n";
    }
    elsif ($new{$_} && $del{$_})
    {
	print STDERR "BAD ERROR: Failed to delete $_\n";
    }
}

foreach $_ (@new)
{
    if ((! $old{$_}) && (! $a_replacement{$_}))
    {
	push(@added,$_);
    }
}

print "The following genomes were deleted:\n\n";
foreach $_ (sort { $a <=> $b } keys(%del))
{
    $name = &name($_,$oldD);
    print "\t$_\t$name\n";
}
print "\n\n";

print "The following genomes were replaced:\n\n";
foreach $from (sort { $a <=> $b } keys(%rep))
{
    $to = $rep{$from};
    print "\t$from\t",&name($from,$oldD),"\n\t\tby\n\t$to\t",&name($to,$newD),"\n================\n\n";
}
print "\n\n";

print "The following genomes were added:\n\n";
foreach $_ (sort { $a <=> $b } @added)
{
    print "\t$_\t",&name($_,$newD),"\n";
}

sub name {
    my($genome,$dir) = @_;

    open(GENOME,"<$dir/Organisms/$genome/GENOME")
	|| confess "$dir does not contain a GENOME file for $genome";
    my $x = <GENOME>;
    chop $x;
    close(GENOME);
    return $x;
}

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