From f5f5a7ae4dcc93fa736b1b2451b17af12f563915 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Thu, 1 Apr 2010 11:08:42 +0000
Subject: [PATCH] When creating a Bio::Seq object, always specify '-alphabet'.
---
modules/Bio/EnsEMBL/Exon.pm | 17 +++++++-----
modules/Bio/EnsEMBL/PredictionTranscript.pm | 12 ++++++---
modules/Bio/EnsEMBL/Transcript.pm | 30 ++++++++++++---------
3 files changed, 35 insertions(+), 24 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index 7024500ed0..47ddd923db 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -1260,10 +1260,11 @@ sub peptide {
$pep_str = $tr->translate->subseq($start, $end);
}
- return Bio::Seq->new(-seq => $pep_str,
- -moltype => 'protein',
- -alphabet => 'protein',
- -id => $self->display_id);
+ return
+ Bio::Seq->new( -seq => $pep_str,
+ -moltype => 'protein',
+ -alphabet => 'protein',
+ -id => $self->display_id );
}
@@ -1309,9 +1310,11 @@ sub seq {
$self->{'_seq_cache'} = $seq;
}
- return Bio::Seq->new(-seq => $self->{'_seq_cache'},
- -id => $self->display_id,
- -moltype => 'dna');
+ return
+ Bio::Seq->new( -seq => $self->{'_seq_cache'},
+ -id => $self->display_id,
+ -moltype => 'dna',
+ -alphabet => 'dna' );
}
diff --git a/modules/Bio/EnsEMBL/PredictionTranscript.pm b/modules/Bio/EnsEMBL/PredictionTranscript.pm
index 2767e5020a..8d00206a32 100644
--- a/modules/Bio/EnsEMBL/PredictionTranscript.pm
+++ b/modules/Bio/EnsEMBL/PredictionTranscript.pm
@@ -277,9 +277,10 @@ sub translation {
$Xseq = "N"x$start_phase . $Xseq;
}
- my $tmpSeq = new Bio::Seq( -id => $self->display_id,
- -seq => $Xseq,
- -moltype => "dna" );
+ my $tmpSeq = new Bio::Seq( -id => $self->display_id,
+ -seq => $Xseq,
+ -moltype => 'dna',
+ -alphabet => 'dna' );
return Bio::EnsEMBL::Translation->new
(-ADAPTOR => $pta,
@@ -335,7 +336,10 @@ sub translate {
# if you want to have a terminal stop codon either comment this line out
# or call translatable seq directly and produce a translation from it
- my $bioseq = new Bio::Seq( -id => $self->display_id, -seq => $dna, -moltype => 'dna' );
+ my $bioseq = new Bio::Seq( -id => $self->display_id,
+ -seq => $dna,
+ -moltype => 'dna',
+ -alphabet => 'dna' );
my $translation = $bioseq->translate(undef,undef,undef,$codon_table_id);
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 89cd813eae..109434c55f 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1405,10 +1405,11 @@ sub five_prime_utr {
return undef if(!$seq);
- return Bio::Seq->new(
- -DISPLAY_ID => $self->display_id,
- -MOLTYPE => 'dna',
- -SEQ => $seq);
+ return
+ Bio::Seq->new( -id => $self->display_id,
+ -moltype => 'dna',
+ -alphabet => 'dna',
+ -seq => $seq );
}
@@ -1439,10 +1440,11 @@ sub three_prime_utr {
return undef if(!$seq);
- return Bio::Seq->new(
- -DISPLAY_ID => $self->display_id,
- -MOLTYPE => 'dna',
- -SEQ => $seq);
+ return
+ Bio::Seq->new( -id => $self->display_id,
+ -moltype => 'dna',
+ -alphabet => 'dna',
+ -seq => $seq );
}
@@ -1626,11 +1628,13 @@ sub translate {
=cut
sub seq {
- my( $self ) = @_;
- return Bio::Seq->new
- (-DISPLAY_ID => $self->display_id,
- -MOLTYPE => 'dna',
- -SEQ => $self->spliced_seq);
+ my ($self) = @_;
+
+ return
+ Bio::Seq->new( -id => $self->display_id,
+ -moltype => 'dna',
+ -alphabet => 'dna',
+ -seq => $self->spliced_seq );
}
--
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