From 58f103c65a4b721c406de5ce0d2f40e5c08e8ae7 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 8 Aug 2012 08:38:23 +0000
Subject: [PATCH] ENSCORESW-232: code does not skip proteins with a *, B, Z and
X any more
---
modules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm | 9 +++------
1 file changed, 3 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm b/modules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm
index 38fff90fc2..be8b1ec32a 100644
--- a/modules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm
@@ -146,13 +146,10 @@ sub dump_translation {
for my $dbid (@translation_ids) {
my $translation = $ta->fetch_by_dbID($dbid);
my $peptide_seq = $translation->seq();
- if ( !($peptide_seq =~ m/[BZX]/ig ) ) {
- if ( $peptide_seq !~ /\n$/ ) {
- $peptide_seq .= "\n";
- }
- $peptide_seq =~ s/\*$//;
- print TMP ">$dbid\n$peptide_seq";
+ if ( $peptide_seq !~ /\n$/ ) {
+ $peptide_seq .= "\n";
}
+ print TMP ">$dbid\n$peptide_seq";
}
close(TMP);
}
--
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