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ensembl-gh-mirror
ensembl
Commits
9c894fca
Commit
9c894fca
authored
Jun 13, 2012
by
Andreas Kusalananda Kähäri
Browse files
Translation stable ID version incrementation only dependent on
translated sequence, not transcript sequence.
parent
3d190b82
Changes
1
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14 deletions
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-14
modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
...Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
+2
-14
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modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblGeneric.pm
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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