Script to be used for detection of obsolete terms in PO, to be used as part of the...

svn path=/; revision=82

diff --git a/interactome_scripts/po_obsolete_check.pl b/interactome_scripts/po_obsolete_check.pl
new file mode 100755 (executable)
index 0000000..a9712ad
--- /dev/null
+++ b/interactome_scripts/po_obsolete_check.pl
@@ -0,0 +1,85 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+##########################################################################
+#   po_obsolete_check.pl                                                 #
+#    Version 0.1                                                         #
+#                                                                        #
+#  Written by Justin Elser, Dept. of BPP, OSU 2011                       #
+#                                                                        #
+#  Program will check the current po obo file for terms that have        #
+#    been obsoleted.  It will then check all association files for       #
+#    annotations linked with those terms and create output files for     #
+#    used for manual intervention by annotation curators.                #
+#                                                                        #
+#  Program should be made part of the SOP when loading new DBs           #
+#                                                                        #
+##########################################################################
+
+#  Use Chris Mungall's GO::Parser to do the searching for is_obsoletes
+use GO::Parser;
+
+# check for arguments and explain usage
+if ($#ARGV !=2) {
+       print "usage: po_obsolete_check.pl OBO_file directory_with_association_files output_file\n";
+       exit;
+}
+
+my $obo_file = $ARGV[0];
+my $assoc_dir = $ARGV[1];
+my $out_file = $ARGV[2];
+
+my @assoc_files = glob("$assoc_dir*.assoc");
+
+# init GO parser
+my $parser = GO::Parser->new({handler=>'obj'});
+$parser->parse($obo_file);
+
+my $ont = $parser->handler->graph;
+
+
+my $obo_terms = $ont->get_all_nodes;
+
+# hash to store obsolete terms
+my %obs_terms_hash;
+
+foreach my $term (@$obo_terms) {
+       if ($term->is_obsolete){
+               my $id = $term->acc;
+               my $name = $term->name;
+               $obs_terms_hash{$id} = $name;
+       }
+}
+
+my %bad_term_hash;
+
+open(output_file, ">$out_file");
+
+foreach my $file (@assoc_files) {
+       open (assoc_file, "$file");
+       my $line_counter = 0;
+       while(<assoc_file>) {
+               my $line = $_;
+               $line_counter++;
+               foreach my $term (keys %obs_terms_hash) {
+                       if ($line =~ $term) {
+                               print  output_file "match found!!!\t$file\t$term\t$line_counter\n";
+                               if(!defined($bad_term_hash{$term})) {
+                                       $bad_term_hash{$term} = 1;
+                               }else{
+                                       my $curr_count = $bad_term_hash{$term};
+                                       $curr_count++;
+                                       $bad_term_hash{$term} = $curr_count;
+                               }
+                       }
+               }
+       }
+}
+               
+foreach my $bad_term (keys %bad_term_hash) {
+       print "$bad_term\t$bad_term_hash{$bad_term}\n";
+}
+
+