From 5f40ce7de6b53a1a653a1431df0e6aab4fd7f974 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Wed, 24 Mar 2004 19:20:18 +0000
Subject: [PATCH] added sanity check and debug print
---
misc-scripts/chimp/human2chimp.pl | 51 ++++++++++++++++++++++++++++---
1 file changed, 47 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/chimp/human2chimp.pl b/misc-scripts/chimp/human2chimp.pl
index 92273ba7cb..50072611a0 100644
--- a/misc-scripts/chimp/human2chimp.pl
+++ b/misc-scripts/chimp/human2chimp.pl
@@ -130,7 +130,14 @@ use Bio::EnsEMBL::Utils::Exception qw(throw info verbose);
foreach my $ftrans (@$finished_transcripts) {
if($ftrans->translation()) {
- print STDERR "\n\n", $ftrans->translate->seq(), "\n\n";
+ my $pep = $ftrans->translate->seq();
+ print STDERR "\n\n$pep\n\n";
+
+ # sanity check, if translation is defined we expect a peptide
+ if(!$pep) {
+ dump_translation($ftrans->translation());
+ throw("Unexpected Translation but no peptide");
+ }
} else {
print STDERR "NO TRANSLATION LEFT\n";
}
@@ -140,6 +147,44 @@ use Bio::EnsEMBL::Utils::Exception qw(throw info verbose);
}
}
+sub dump_translation {
+ my $tl = shift;
+
+ print STDERR "TRANSLATION\n";
+
+ if(!$tl) {
+ print STDERR " undef\n";
+ return;
+ }
+
+ if($tl->start_Exon()) {
+ print STDERR " start exon = ", $tl->start_Exon->stable_id, "\n";
+ } else {
+ print STDERR " start exon = undef\n";
+ }
+
+ if($tl->end_Exon()) {
+ print STDERR " end exon = ", $tl->end_Exon->stable_id, "\n";
+ } else {
+ print STDERR " end exon = undef\n";
+ }
+
+ if(defined($tl->start())) {
+ print STDERR " start = ", $tl->start(), "\n";
+ } else {
+ print STDERR " start = undef\n";
+ }
+
+ if(defined($tl->end())) {
+ print STDERR " end = ", $tl->end(), "\n";
+ } else {
+ print STDERR " end = undef\n";
+ }
+
+
+ return;
+}
+
###############################################################################
#
@@ -242,8 +287,6 @@ sub transfer_transcript {
my $num = scalar(@coords);
- # save exon length before we go splitting exons etc.:
-
for (my $i=0; $i < $num; $i++) {
my $c = $coords[$i];
@@ -297,7 +340,7 @@ sub transfer_transcript {
$chimp_cdna_pos += $c->length();
}
} # foreach coord
- }
+ }
}
$cdna_exon_start = $chimp_cdna_pos + 1;
--
GitLab