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ensembl-gh-mirror
ensembl
Commits
e595a961
Commit
e595a961
authored
Aug 06, 2013
by
Alessandro Vullo
Browse files
Method optimisation removing multiple calls to the same method with no apparent reason
parent
3ca76e1a
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1
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5 deletions
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-5
modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
+2
-5
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modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
View file @
e595a961
...
...
@@ -69,7 +69,6 @@ sub print_feature {
my
@endcs
=
$self
->
_make_stop_codon_features
(
$transcript
);
my
(
$hasstart
,
$hasend
)
=
$self
->
_check_start_and_stop
(
$transcript
);
# TODO: ask Andy if this is safe
my
$dbname
=
$transcript
->
adaptor
()
->
dbc
()
->
dbname
();
my
$vegadb
=
$dbname
=~
/vega/
;
my
$gene
=
$transcript
->
get_Gene
();
...
...
@@ -165,7 +164,7 @@ sub print_feature {
$exon
==
$transcript
->
translation
->
start_Exon
&&
$hasstart
)
{
my
$tmpcnt
=
$count
;
foreach
my
$startc
(
@startcs
)
{
# here we should check the start codon covers 3 bases
# here we should check the start codon covers 3 bases
print
$fh
$idstr
.
"
\t
"
.
$transcript_biotype
.
"
\t
"
.
'
start_codon
'
.
"
\t
"
.
...
...
@@ -272,8 +271,6 @@ sub _make_start_codon_features {
return
(())
unless
$trans
->
translation
;
my
@translateable
=
@
{
$trans
->
get_all_translateable_Exons
};
my
@pepgencoords
=
$trans
->
pep2genomic
(
1
,
1
);
# cdna can come padded these days so allow gap at the start
...
...
@@ -292,7 +289,7 @@ sub _make_start_codon_features {
throw
(
sprintf
"
Pep start (end of) for transcript %s maps to gap
",
$trans
->
display_id
);
}
@translateable
=
@
{
$trans
->
get_all_translateable_Exons
};
my
@translateable
=
@
{
$trans
->
get_all_translateable_Exons
};
my
@startc_feat
;
my
$phase
=
0
;
foreach
my
$pepgencoord
(
@pepgencoords
)
{
...
...
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