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ensembl-gh-mirror
ensembl
Commits
656baf98
Commit
656baf98
authored
May 21, 2010
by
Ian Longden
Browse files
Take possible N-padding at beginning of CDS into account for the mapping.
parent
c8211a77
Changes
1
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9 additions
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1 deletion
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-1
modules/Bio/EnsEMBL/TranscriptMapper.pm
modules/Bio/EnsEMBL/TranscriptMapper.pm
+9
-1
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modules/Bio/EnsEMBL/TranscriptMapper.pm
View file @
656baf98
...
...
@@ -136,7 +136,10 @@ sub _load_mapper {
my
$edit_shift
=
0
;
my
$cdna_start
=
undef
;
my
$cdna_end
=
0
;
# 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
})
{
my
$gen_start
=
$ex
->
start
();
...
...
@@ -320,6 +323,11 @@ sub pep2genomic {
$start
=
3
*$start
-
2
+
(
$self
->
{'
cdna_coding_start
'}
-
1
)
-
$shift
;
$end
=
3
*$end
+
(
$self
->
{'
cdna_coding_start
'}
-
1
)
-
$shift
;
print
"
start is
$start
end is
$end
shift is
$shift
cdna_coding_start is
"
.
$self
->
{'
cdna_coding_start
'}
.
"
\n
";
# if($start < 1){
# $start = 1;
# }
# print "start is $start end is $end shift is $shift cdna_coding_start is ".$self->{'cdna_coding_start'}."\n";
return
$self
->
cdna2genomic
(
$start
,
$end
);
}
...
...
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