From 5e61b532091f96b34c395b2389ff3394fd25b667 Mon Sep 17 00:00:00 2001
From: Kevin Howe <klh@ebi.ac.uk>
Date: Tue, 23 Jan 2007 14:56:26 +0000
Subject: [PATCH] Omit D_segment and J_segment genes from the dump, thus
excluding them from the sequence-match xref pipeline (they are too for this
to be sensible)
---
misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm | 3 +++
1 file changed, 3 insertions(+)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 242a054729..c1c81a85a3 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -595,6 +595,9 @@ sub fetch_and_dump_seq{
my $i =0;
my $rna = 0;
foreach my $gene (@genes){
+ next if $gene->biotype eq 'J_segment';
+ next if $gene->biotype eq 'D_segment';
+
foreach my $transcript (@{$gene->get_all_Transcripts()}) {
$i++;
my $seq = $transcript->spliced_seq();
--
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