Add section that skips T.cacao transcripts

svn path=/; revision=613

diff --git a/interactome_scripts/inparanoid_output_parse.pl b/interactome_scripts/inparanoid_output_parse.pl
index 0e0983f8b868470bc29c9b70c80f9458d6aab74f..f481e05e08517742274c9886835bd3ae1714c000 100755 (executable)
--- a/interactome_scripts/inparanoid_output_parse.pl
+++ b/interactome_scripts/inparanoid_output_parse.pl
@@ -156,6 +156,12 @@ foreach my $input_file (@files) {
                                                next if ($gene =~ /\_T0[2-9]$/);
                                                next if ($gene =~ /\_T1[0-9]$/);
                                }
+                               
+                               # skip Theobroma genes that are not the first transcript
+                               if($species eq "Theobroma_cacao") {
+                                               next if ($gene =~ /t[2-9]$/);
+                                               next if ($gene =~ /t1[0-9]$/);
+                               }
                }
        
                if(!defined($id_hash{$clust_id})) {