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Revision 1.4 - (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 1.3: +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.
#


$0 =~ m/([^\/]+)$/;
$usage = "$1  tbl changes";

=pod

=head1 alter_tbl

Takes a TBL file and a set of changes computed by `check_starts_for_pegs`
to produce an altered TBL file.

(NOTE: The function of this script partially overlaps `TransactFeatures.pl`,
and this script should probably be retired once the `TransactFeatures.pl`
procedure is finalized and fully documented.)

=cut


(($tbl     = shift) && (-s $tbl))
    || die "tbl file $tbl does not exist\n\n\tusage: $usage\n\n";
(($changes = shift) && (-s $changes)) 
    || die "start-changes file $changes does not exist\n\n\tusage: $usage\n\n";

open(CHANGES, "<$changes") || die "Could not read-open $changes";
while(defined($entry = <CHANGES>))
{
    ($id, $old_locus, $new_locus) = split /\t/, $entry;
    
    if (not defined($map{$old_locus}))
    {
	$map{$old_locus} = [$id, $new_locus];
    }
    else
    {
	die "Duplicate change entry $entry";
    }
}
close(CHANGES) || die "Could not close $changes";


open(OLD_TBL, "<$tbl") || die "Could not read-open old tbl $tbl~";
while (defined($entry = <OLD_TBL>))
{
    chomp $entry;
    ($id, $locus, @rest) = split /\t/, $entry;
    
    if (defined($map{$locus}))
    {
	if ($id eq $map{$locus}->[0])
	{
	    print  join("\t", ($id, $map{$locus}->[1], @rest)), "\n";
	}
	else
	{
	    die "FID mismatch for locus=$map{$locus}->[1], ID=$map{$locus}->[0], record:\n$entry\n";
	}
    }
    else
    {
	print  "$entry\n";
    }
}
close(OLD_TBL) || die "Could not close $tbl~";

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