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Revision 1.3 - (download) (as text) (annotate)
Fri Sep 15 11:25:42 2006 UTC (13 years, 3 months ago) by overbeek
Branch: MAIN
Changes since 1.2: +2 -0 lines
fix yet another bug in all_bbhs - this one relating to deleted_fids

# -*- 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.
#

use FIG;
my $fig = new FIG;

use NewGenome;
use ToCall;

my $usage = "usage: promote_orfs_to_pegs To_Call_Dir";

if (@ARGV && ($ARGV[0] =~ m/-h(elp)?/)) {
    print STDERR "\n   $usage\n\n";
    exit (0);
}

my ($to_call_dir);

(
 ($to_call_dir = shift @ARGV)
)
    || die "\n   $usage\n\n";

$to_call_dir =~ s/\/$//o;

my $to_call;
$to_call = new NewGenome($to_call_dir,"all");
$to_call->promote_remaining_orfs;
$to_call->export_features;

if (!-s "$to_call_dir/Features/orf/tbl") {
    &FIG::run("rm -fR $to_call_dir/Features/orf");
}
else {
    die "Something is wrong --- $to_call_dir/Features/orf/tbl is non-empty";
}

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