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Revision 1.1 - (download) (as text) (annotate)
Fri Mar 17 00:29:39 2006 UTC (13 years, 8 months ago) by overbeek
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, 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, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Removes duplicate entries from tbl file. -- /gdp

# -*- 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 < old.tbl > purged.tbl";

die "\n\n\tusage: $usage\n\n" if ($ARGV[0] && ($ARGV[0] =~ m/^--?h/));

while (defined($entry = <STDIN>))
{
    chomp $entry;
    ($id, $locus) = split /\t/, $entry;
    
    $locus =~ m/^([^,]+)_(\d+)_\d+/;
    ($contig, $beg) = ($1, $2);
    
    $locus =~ m/\S+_\d+_(\d+)$/;
    $end   =  $1;
    
    $tbl{$id} = [$entry, $contig, &min($beg, $end)];
}
foreach $_ (sort {  ($tbl{$a}->[1] cmp $tbl{$b}->[1])
		 || ($tbl{$a}->[2] <=> $tbl{$b}->[2]) } keys %tbl)
{
    print "$tbl{$_}->[0]\n";
}
exit(0);

sub min { my ($x, $y) = @_; return (($x < $y) ? $x : $y); }

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