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ensembl-gh-mirror
ensembl
Commits
9c894fca
Commit
9c894fca
authored
12 years ago
by
Andreas Kusalananda Kähäri
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Translation stable ID version incrementation only dependent on
translated sequence, not transcript sequence.
parent
3d190b82
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1 changed file
modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
+2
-14
2 additions, 14 deletions
...Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
with
2 additions
and
14 deletions
modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
+
2
−
14
View file @
9c894fca
...
...
@@ -255,7 +255,7 @@ sub is_valid {
genes, the rules for incrementing the version number are:
- exons: if exon sequence changed
- transcript: if spliced exon sequence changed
- translation: if trans
cript or translation
changed
- translation: if trans
lated sequence
changed
- gene: if any of its transcript changed
Return type : String - the version to be used
Exceptions : thrown on wrong argument
...
...
@@ -280,19 +280,7 @@ sub calculate_version {
}
elsif
(
$s_obj
->
isa
('
Bio::EnsEMBL::IdMapping::TinyTranslation
')
)
{
# increment version if transcript or translation sequences changed
my
$s_tr
=
$self
->
cache
->
get_by_key
(
'
transcripts_by_id
',
'
source
',
$s_obj
->
transcript_id
()
);
my
$t_tr
=
$self
->
cache
->
get_by_key
(
'
transcripts_by_id
',
'
target
',
$t_obj
->
transcript_id
()
);
if
(
$s_tr
->
seq_md5_sum
()
ne
$t_tr
->
seq_md5_sum
()
||
$s_obj
->
seq
()
ne
$t_obj
->
seq
()
)
{
++
$version
;
}
if
(
$s_obj
->
seq
()
ne
$t_obj
->
seq
()
)
{
++
$version
}
}
elsif
(
$s_obj
->
isa
('
Bio::EnsEMBL::IdMapping::TinyGene
')
)
{
# increment version if any transcript changed
...
...
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