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Revision 1.3 - (download) (as text) (annotate)
Thu Apr 17 20:48:15 2008 UTC (11 years, 7 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 1.2: +2 -1 lines
Introduct &FIG::get_figfams_data()

#!/usr/bin/env /Volumes/seagate/FIGdisk/env/mac/bin/perl

BEGIN {
    @INC = qw(
              /Volumes/seagate/FIGdisk/dist/releases/ross/mac/lib
              /Volumes/seagate/FIGdisk/dist/releases/ross/mac/lib/FigKernelPackages
              /Volumes/seagate/FIGdisk/dist/ross/mac/lib
              /Volumes/seagate/FIGdisk/dist/ross/mac/lib/FigKernelPackages
              /Volumes/seagate/FIGdisk/env/mac/lib/perl5/5.8.7/darwin-2level
              /Volumes/seagate/FIGdisk/env/mac/lib/perl5/5.8.7
              /Volumes/seagate/FIGdisk/env/mac/lib/perl5/site_perl/5.8.7/darwin-2level
              /Volumes/seagate/FIGdisk/env/mac/lib/perl5/site_perl/5.8.7
              /Volumes/seagate/FIGdisk/env/mac/lib/perl5/site_perl
              .
              /Volumes/seagate/FIGdisk/config
 
);
}
use Data::Dumper;
use Carp;
use FIG_Config;
$ENV{'BLASTMAT'} = "/Volumes/seagate/FIGdisk/BLASTMAT";
$ENV{'FIG_HOME'} = "/Volumes/seagate/FIGdisk";
# end of tool_hdr
########################################################################

use FIG;
my $fig = new FIG;

my($user,$genome,$contextF,$hit,$peg,$func,$curr);
my $usage = "usage: install_anticipated_functions User GenomeID ContextFile";
(
 ($user      = shift @ARGV) &&
 ($genome    = shift @ARGV) &&
 ($contextF  = shift @ARGV) && (-s $contextF)
)
    || die $usage;

$user =~ s/^master://i;

my $tmpF = "$FIG_Config::temp/matched.families.$$";
my $ffdata = &FIG::get_figfams_data();
system "find_genes_based_on_neighbors $ffdata $FIG_Config::organisms/$genome $tmpF < $contextF > /dev/null 2> /dev/null";

my $changes = 0;
foreach $hit (`cat $tmpF`)
{
    if ($hit =~ /^\S+\t(\S+)\t(\S.*\S)/)
    {
	$peg  = $1;
	$func = $2;
	$curr = $fig->function_of($peg);
	if ($curr ne $func)
	{
	    print STDERR "changing annotation for $peg from\n$\tcurr\nto\n\t$func\n\n";
	    $changes++;
	    $fig->assign_function($peg,$user,$func,"");
	    if ($curr)
	    {
		$fig->add_annotation($peg,$user,"Set function to\n$func\n\nIt used to be $curr, but got changed using FIGfams\n");
	    }
	    else
	    {
		$fig->add_annotation($peg,$user,"Set function to\n$func\n\nDecision made using FIGfams");
	    }
	}
    }
}
unlink($tmpF);

print STDERR "Made $changes new assignments\n";


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