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ensembl-gh-mirror
ensembl
Commits
e4e065a5
Commit
e4e065a5
authored
20 years ago
by
Graham McVicker
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made translateable_seq() and translate() more careful about the possible absence of Translation
parent
949abb12
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1 changed file
modules/Bio/EnsEMBL/Transcript.pm
+12
-2
12 additions, 2 deletions
modules/Bio/EnsEMBL/Transcript.pm
with
12 additions
and
2 deletions
modules/Bio/EnsEMBL/Transcript.pm
+
12
−
2
View file @
e4e065a5
...
...
@@ -426,6 +426,10 @@ sub spliced_seq {
sub
translateable_seq
{
my
(
$self
)
=
@_
;
if
(
!
$self
->
translation
())
{
return
'';
}
my
$mrna
=
$self
->
spliced_seq
();
my
$start
=
$self
->
cdna_coding_start
();
my
$end
=
$self
->
cdna_coding_end
();
...
...
@@ -1099,8 +1103,10 @@ sub get_all_translateable_Exons {
Example : none
Description: return the peptide (plus eventuel stop codon) for this
transcript. Does N padding of non phase matching exons.
It uses translateable_seq internally.
Returntype : Bio::Seq
It uses translateable_seq internally.
Returns undef if this Transcript does not have a translation
(i.e. pseudogene).
Returntype : Bio::Seq or undef
Exceptions : If no Translation is set in this Transcript
Caller : general
...
...
@@ -1109,6 +1115,10 @@ sub get_all_translateable_Exons {
sub
translate
{
my
(
$self
)
=
@_
;
if
(
!
$self
->
translation
())
{
return
undef
;
}
my
$mrna
=
$self
->
translateable_seq
();
my
$display_id
;
if
(
defined
$self
->
translation
->
stable_id
)
{
...
...
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