From c7a3ccfaa2c3a07690974b03b1021ac260a610ec Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Wed, 24 Mar 2004 19:16:40 +0000
Subject: [PATCH] *fixed coding end setting bug (off by one in comparison) *do
not create translation if less than 3 nucl. left in CDS
---
misc-scripts/chimp/Transcript.pm | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/chimp/Transcript.pm b/misc-scripts/chimp/Transcript.pm
index 9779ca0b7c..62794ec93a 100644
--- a/misc-scripts/chimp/Transcript.pm
+++ b/misc-scripts/chimp/Transcript.pm
@@ -277,7 +277,7 @@ sub split_itrans {
throw("unexpected: could not find bad exon in transcript");
}
- debug("==BAD EXON: (keep = $keep_exon)\n");
+ debug("==BAD EXON: ". (($keep_exon) ? 'keeping' : 'discarding'));
print_exon($bad_exon);
# keep the 'bad exon' if the flag was set
@@ -311,7 +311,7 @@ sub split_itrans {
$first_trans->cdna_coding_start(1);
$first_trans->cdna_coding_end(0);
}
- elsif($last_ex->cdna_end() > $first_trans->cdna_coding_start() &&
+ elsif($last_ex->cdna_end() >= $first_trans->cdna_coding_start() &&
$last_ex->cdna_end() < $first_trans->cdna_coding_end()) {
# coding sequence is cut by coding end
$first_trans->cdna_coding_end($last_ex->cdna_end());
@@ -384,7 +384,8 @@ sub make_Transcript {
my $translation;
# the whole translation may have been deleted
- if ($itrans->cdna_coding_start == $itrans->cdna_coding_end + 1) {
+ # discard translation if mrna is less than a codon in length
+ if($itrans->cdna_coding_end - $itrans->cdna_coding_start + 1 < 3) {
$translation = undef;
} else {
$translation = Bio::EnsEMBL::Translation->new();
@@ -442,6 +443,7 @@ sub make_Transcript {
print_exon($itrans->get_all_Exons->[0]);
print STDERR "LAST EXON:\n";
print_exon($itrans->get_all_Exons->[-1], $itrans);
+ throw("Unexpected: Could not find translation start exon in transcript\n");
}
if($translation && !$translation->end_Exon()) {
print STDERR "Could not find translation end exon in transcript.\n";
@@ -449,6 +451,7 @@ sub make_Transcript {
print_exon($itrans->get_all_Exons->[0]);
print STDERR "LAST EXON:\n";
print_exon($itrans->get_all_Exons->[-1], $itrans);
+ throw("Unexpected: Could not find translation end exon in transcript\n");
}
return $transcript;
--
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