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ensembl-gh-mirror
ensembl
Commits
c8c66c95
Commit
c8c66c95
authored
May 21, 2010
by
Ian Longden
Browse files
phase not set yet so need to pass it
parent
656baf98
Changes
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4 additions
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3 deletions
+4
-3
modules/Bio/EnsEMBL/TranscriptMapper.pm
modules/Bio/EnsEMBL/TranscriptMapper.pm
+4
-3
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modules/Bio/EnsEMBL/TranscriptMapper.pm
View file @
c8c66c95
...
...
@@ -88,8 +88,6 @@ sub new {
throw
("
Transcript argument is required.
");
}
# Create a cdna <-> genomic mapper and load it with exon coords
my
$mapper
=
_load_mapper
(
$transcript
);
my
$exons
=
$transcript
->
get_all_Exons
();
my
$start_phase
;
...
...
@@ -99,6 +97,9 @@ sub new {
$start_phase
=
-
1
;
}
# Create a cdna <-> genomic mapper and load it with exon coords
my
$mapper
=
_load_mapper
(
$transcript
,
$start_phase
);
my
$self
=
bless
({'
exon_coord_mapper
'
=>
$mapper
,
'
start_phase
'
=>
$start_phase
,
'
cdna_coding_start
'
=>
$transcript
->
cdna_coding_start
(),
...
...
@@ -122,6 +123,7 @@ sub new {
sub
_load_mapper
{
my
$transcript
=
shift
;
my
$start_phase
=
shift
;
my
$mapper
=
Bio::EnsEMBL::
Mapper
->
new
(
'
cdna
',
'
genomic
');
...
...
@@ -138,7 +140,6 @@ sub _load_mapper {
my
$cdna_start
=
undef
;
# Take possible N-padding at beginning of CDS into account.
my
$start_phase
=
$self
->
{'
start_phase
'};
my
$cdna_end
=
(
$start_phase
>
0
)
?
$start_phase
:
0
;;
foreach
my
$ex
(
@
{
$transcript
->
get_all_Exons
})
{
...
...
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