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Revision 1.11 - (download) (as text) (annotate)
Mon Sep 17 20:15:19 2007 UTC (12 years, 6 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, 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
Changes since 1.10: +1 -1 lines
bugfix

# -*- 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: index_annotations

use FIG;
use Tracer;

my $fig = new FIG;

my @genomes;
my $reload;
if (@ARGV == 0)
{
    $reload++;
    @genomes = $fig->genomes;
}
else
{
    @genomes = @ARGV;
}

my($offset1,$offset2,$peg,$ln);
Trace("Indexing annotations.") if T(2);
my $relTable = "$FIG_Config::temp/tmp$$.seeks";
Open(\*RELTABLE, ">$relTable");

foreach $genome (@genomes) {
    Trace("Indexing genome $genome.") if T(3);
    my $fileno = $fig->file2N("$FIG_Config::organisms/$genome/annotations");

    if ((-s "$FIG_Config::organisms/$genome/annotations") && 
        open(FILE,"<$FIG_Config::organisms/$genome/annotations")) {
        $/ = "\n//\n";
        $offset1 = tell FILE;
        while (defined($line = <FILE>))
        {
            if ($line =~ /^(fig\|\d+\.\d+\.[a-zA-Z]{2,10}\.\d+)\n(\d+)\n(\S+)\n(.*)/s)
            {
                $peg = $1;
                $date = $2;
                $who  = $3;
                $body = $4;
                $ma   = ($body =~ /^Set master function to/);
                # Modified for Windows compatibility
                $ln = length($line) - 3;
                print RELTABLE "$peg\t$date\t$who\t$ma\t$fileno\t$offset1\t$ln\n";
            }
            $offset1 = tell FILE;
        }
        close(FILE);
        $/ = "\n";
    }
    elsif (-s "$FIG_Config::organisms/$genome/annotations")
    {
        Trace("WARNING: could not open $FIG_Config::organisms/$genome/annotations") if T(1);
    }

}
close(RELTABLE);

if ($reload)
{
    $fig->reload_table('all', "annotation_seeks",
		       "fid varchar(32) NOT NULL, dateof INTEGER, who varchar(32), "
		       . "ma char, fileno INTEGER, seek INTEGER, len INTEGER",
		   { annotations_fig_ix => "fid", annotations_who_ix => "who",
			 annotations_dateof_ix => "dateof" },
		       $relTable);
}
else
{
    my $db = $fig->db_handle();
    my $cond = join(" OR ", map { "fid LIKE 'fig|$_.%'" } @genomes);
    $db->SQL(qq(DELETE FROM annotation_seeks
		WHERE $cond));
    $db->load_table(file => $relTable,
		    tbl => 'annotation_seeks');
}
    
unlink($relTable);

undef $fig;
Trace("Annotations indexed.") if T(2);

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