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Revision 1.6 - (download) (as text) (annotate)
Fri Jan 27 18:59:26 2006 UTC (14 years 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 1.5: +1 -1 lines
bugfix.

########################################################################
#
# 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;

my $usage = "usage: salvage_annotations From To Map";  

(
 ($from = shift @ARGV) &&
 ($to   = shift @ARGV) &&
 ($map  = shift @ARGV)
)
    || die $usage;

($from =~ /(\d+\.\d+)$/) || die "$from does not end in the organism ID";
my $fromO = $1;

($to =~ /(\d+\.\d+)$/) || die "$to does not end in the organism ID";
my $toO = $1;

%mapping = map { $_ =~ /^(\S+)\t(\S+)/; $1 => $2 } `cat $map`;

&salvage_assignments("$from/assigned_functions","$to/assigned_functions",\%mapping);
&salvage_annotations("$from/annotations","$to/annotations",\%mapping);

sub salvage_assignments {
    my($in,$out,$mapping) = @_;
    my($rep);

    open(IN,"<$in") || die "could not open $in";
    open(OUT,">$out") || die "could not open $out";
    while (defined($_ = <IN>))
    {
	if (($_ =~ /^(\S+)\t(\S.*\S)/) && ($rep = $mapping->{$1}))
	{
	    print OUT "$rep\t$2\n";
	}
    }
    close(IN);
    close(OUT);
}

sub salvage_annotations {
    my($in,$out,$mapping) = @_;
    my($rep);
 
    open(IN,"<$in") || die "could not open $in";
    open(OUT,">$out") || die "could not open $out";
    $/ = "\n//\n";
    while (defined($_ = <IN>))
    {
	if (($_ =~ /^(\S+)\n(\S.*\S)/s) && ($rep = $mapping->{$1}))
	{
	    print OUT "$rep\n$2\n";
	}
    }
    $/ = "\n";;
    close(IN);
    close(OUT);
}

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