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Revision 1.2 - (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 1.1: +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.
#


# usage: fix_annotations [-trace=N]

use FIG;
use Tracer;
use File::Copy;
use Stats;


my($offset1,$offset2,$peg,$ln,$tLevel);
if ($ARGV[0] =~ /^-trace=(\d+)$/) {
    $tLevel = $1;
} else {
    $tLevel = 3;
}
TSetup("$tLevel FIG Tracer", "TEXT");
Trace("Fixing annotations.") if T(2);
my $stats = Stats->new();
my $fig = new FIG;

foreach $genome ($fig->genomes) {
    Trace("Fixing genome $genome.") if T(3);
    $stats->Add("genome");
    my $fileName = "$FIG_Config::organisms/$genome/annotations";
    my $fixedFile = "$FIG_Config::temp/tmp$$.fixes";

    if ((-s $fileName) && open(FILE,"<$fileName")) {
        Open(\*FIXFILE, ">$fixedFile");
        $/ = "\n//\n";
        my $fixed = 0;
        while (defined($line = <FILE>))
        {
            if ($line =~ /^(fig\|\d+\.\d+\.[a-zA-Z]{2,10}\.\d+)\n(\d+)\n(\S*)\n(.*)/s)
            {
                $stats->Add("annotation");
                my $peg = $1;
                my $date = $2;
                my $who;
                if ($3) {
                    $who = $3;
                } else {
                    $who = "fig";
                    $stats->Add("userFix");
                    $fixed = 1;
                }
                my $body = $4;
                print FIXFILE "$peg\n$date\n$who\n$body\n//\n";
            }
        }
        close(FILE);
        $/ = "\n";
        if ($fixed) {
            move($fileName, "$fileName~");
            move($fixedFile, $fileName);
            $stats->Add("fileFixed");
        } else {
            unlink $fixedFile;
        }
    }
    elsif (-s "$FIG_Config::organisms/$genome/annotations")
    {
        Trace("WARNING: could not open $FIG_Config::organisms/$genome/annotations") if T(1);
    }

}
close(FIXFILE);    

undef $fig;
Trace("Statistics for run:\n\n" . $stats->Show() . "\n") if T(2);
Trace("Annotations fixed.") if T(2);

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