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ensembl-gh-mirror
ensembl
Commits
f5f5a7ae
Commit
f5f5a7ae
authored
Apr 01, 2010
by
Andreas Kusalananda Kähäri
Browse files
When creating a Bio::Seq object, always specify '-alphabet'.
parent
70a8f0fa
Changes
3
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3 changed files
with
35 additions
and
24 deletions
+35
-24
modules/Bio/EnsEMBL/Exon.pm
modules/Bio/EnsEMBL/Exon.pm
+10
-7
modules/Bio/EnsEMBL/PredictionTranscript.pm
modules/Bio/EnsEMBL/PredictionTranscript.pm
+8
-4
modules/Bio/EnsEMBL/Transcript.pm
modules/Bio/EnsEMBL/Transcript.pm
+17
-13
No files found.
modules/Bio/EnsEMBL/Exon.pm
View file @
f5f5a7ae
...
...
@@ -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
'
);
}
...
...
modules/Bio/EnsEMBL/PredictionTranscript.pm
View file @
f5f5a7ae
...
...
@@ -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
);
...
...
modules/Bio/EnsEMBL/Transcript.pm
View file @
f5f5a7ae
...
...
@@ -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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