From bd31839b654bf45c2875eec969586ca9dd45a98a Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Tue, 17 Feb 2015 00:41:57 +0000
Subject: [PATCH] Add section that skips T.cacao transcripts

svn path=/; revision=613
---
 interactome_scripts/inparanoid_output_parse.pl | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/interactome_scripts/inparanoid_output_parse.pl b/interactome_scripts/inparanoid_output_parse.pl
index 0e0983f..f481e05 100755
--- 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})) {
-- 
2.34.1