From a8b625776e8a597aef9bbcc3bcf81809abe246e7 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Sun, 22 Feb 2004 18:01:21 +0000
Subject: [PATCH] few typos
---
misc-scripts/chimp/Deletion.pm | 10 +++++-----
misc-scripts/chimp/InterimTranscript.pm | 2 +-
misc-scripts/chimp/human2chimp.pl | 7 +++----
3 files changed, 9 insertions(+), 10 deletions(-)
diff --git a/misc-scripts/chimp/Deletion.pm b/misc-scripts/chimp/Deletion.pm
index e430b8eac8..c1c62858fe 100644
--- a/misc-scripts/chimp/Deletion.pm
+++ b/misc-scripts/chimp/Deletion.pm
@@ -101,12 +101,12 @@ sub process_delete {
}
###############################################################################
-# process_five_prime_utr_deletion
+# process_five_prime_utr_delete
#
# processes a deletion in the five prime utr of a transcript
###############################################################################
-sub process_five_prime_utr_deletion {
+sub process_five_prime_utr_delete {
my $cdna_del_pos_ref = shift;
my $del_len = shift;
my $exon = shift;
@@ -125,12 +125,12 @@ sub process_five_prime_utr_deletion {
}
###############################################################################
-# process_three_prime_utr_deletion
+# process_three_prime_utr_delete
#
# processes a deletion in the three prime utr of a transcript
###############################################################################
-sub process_three_prime_utr_deletion {
+sub process_three_prime_utr_delete {
my $cdna_del_pos_ref = shift;
my $del_len = shift;
my $exon = shift;
@@ -152,7 +152,7 @@ sub process_three_prime_utr_deletion {
# processes a deletion in the cds of a transcript
###############################################################################
-sub process_cds_deletion {
+sub process_cds_delete {
my $cdna_del_pos_ref = shift;
my $del_len = shift;
my $exon = shift;
diff --git a/misc-scripts/chimp/InterimTranscript.pm b/misc-scripts/chimp/InterimTranscript.pm
index d782f12e55..b6c8947cf8 100644
--- a/misc-scripts/chimp/InterimTranscript.pm
+++ b/misc-scripts/chimp/InterimTranscript.pm
@@ -39,7 +39,7 @@ sub add_Exon {
sub get_all_Exons {
my $self = shift;
- return @{$self->{'exons'}};
+ return $self->{'exons'};
}
diff --git a/misc-scripts/chimp/human2chimp.pl b/misc-scripts/chimp/human2chimp.pl
index 5df4c7c118..bd1dc290dd 100644
--- a/misc-scripts/chimp/human2chimp.pl
+++ b/misc-scripts/chimp/human2chimp.pl
@@ -187,9 +187,9 @@ sub transfer_transcript {
my $entire_delete = 1;
- Deletion::process_entire_delete(\$chimp_cdna_pos, $c->length(),
- $chimp_exon,
- $chimp_transcript, $entire_delete);
+ Deletion::process_delete(\$chimp_cdna_pos, $c->length(),
+ $chimp_exon,
+ $chimp_transcript, $entire_delete);
$chimp_exon->fail(1);
$chimp_transcript->add_Exon($chimp_exon);
@@ -442,7 +442,6 @@ sub create_transcripts {
my $stat_msg = StatMsg->new(StatMsg::TRANSCRIPT | StatMsg::SCAFFOLD_SPAN);
$itranscript->add_StatMsg($stat_msg);
### TBD can probably split transcript rather than discarding
- $itranscript->fail(1);
return;
}
--
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