From f0eff3b488301ef68b392af6193a15166115294b Mon Sep 17 00:00:00 2001
From: Kevin Howe <klh@ebi.ac.uk>
Date: Tue, 16 Dec 2014 11:49:15 +0000
Subject: [PATCH] Fixed bug with replacement of petpide ambiguity chars with X
---
misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm | 1 +
1 file changed, 1 insertion(+)
diff --git a/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm b/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
index bf04e2cbd8..e0f66f11a5 100644
--- a/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm
@@ -340,6 +340,7 @@ sub dump_xref{
$sth->execute();
while(my @row = $sth->fetchrow_array()){
# Ambiguous peptides must be cleaned out to protect Exonerate from J,O and U codes
+ $row[1] = uc($row[1]);
$row[1] =~ s/(.{60})/$1\n/g;
if ($sequence_type eq 'peptide') { $row[1] =~ tr/JOU/X/ }
print $DH ">".$row[0]."\n".$row[1]."\n";
--
GitLab