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Revision 1.3 - (download) (as text) (annotate)
Mon Jun 16 15:42:50 2008 UTC (11 years, 5 months ago) by mkubal
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, 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, 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: +1 -0 lines
provides usage when no argument given

use FIG;
use lib PPO;
use lib Ontology;
use DBMaster;

my $sqlite_db = shift(@ARGV);
if(!$sqlite_db){print "#usage make_cdd_ontology sqlite_database_file\n"; exit;}
my $dbmaster = DBMaster->new(-database => $sqlite_db, -backend => 'SQLite');

`cp /vol/biodb/cdd/cddid.tbl.gz /vol/ontologies/temp`;
`gunzip /vol/ontologies/temp/cddid.tbl.gz`;

open(IN,"/vol/ontologies/temp/cddid.tbl");
while($_ = <IN>){
    chomp($_);
    if($_ =~/^\d+/){
	my @parts = split("\t",$_);
	my $id = $parts[0];
	my $term = $parts[2];
	my $description = $parts[3];
	
	my ($dt_objs,$dt_obj);
	$dt_objs =  $dbmaster->cdd->get_objects( { 'id' => $id } );
	print "term:$term\n";
	if(scalar(@$dt_objs) == 0){ 
	   $dt_obj = $dbmaster->cdd->create( { 'id'    => $id,
					      'term' => $term,
					      'description' => $description
					       } );
       }
    }
}

`rm -f /vol/ontologies/temp/cddid* `;

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