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Tamara El Naboulsi
ensembl
Commits
e6082ac8
Commit
e6082ac8
authored
11 years ago
by
Alessandro Vullo
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Added method print_feature
parent
647a7b31
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modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
+26
-2
26 additions, 2 deletions
modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
with
26 additions
and
2 deletions
modules/Bio/EnsEMBL/Utils/IO/GTFSerializer.pm
+
26
−
2
View file @
e6082ac8
...
...
@@ -27,17 +27,41 @@ for the GTF format.
=cut
package
Bio::EnsEMBL::Utils::IO::
G
F
FSerializer
;
package
Bio::EnsEMBL::Utils::IO::
G
T
FSerializer
;
use
strict
;
use
warnings
;
use
Bio::EnsEMBL::Utils::
Exception
;
use
Bio::EnsEMBL::Utils::IO::
FeatureSerializer
;
use
Bio::EnsEMBL::Utils::
Scalar
qw/
assert_ref
check_ref/
;
use
Bio::EnsEMBL::Utils::
Scalar
qw/check_ref/
;
use
base
qw(Bio::EnsEMBL::Utils::IO::FeatureSerializer)
;
my
%strand_conversion
=
(
'
1
'
=>
'
+
',
'
0
'
=>
'
?
',
'
-1
'
=>
'
-
');
=head2 print_feature
Arg [1] : Bio::EnsEMBL::Transcript
Example : $serializer->print_feature($transcript)
Description:
Returntype : none
=cut
sub
print_feature
{
my
$self
=
shift
;
my
$feature
=
shift
;
throw
(
sprintf
"
Feature is of type %s. Cannot write non transcripts to GTF
",
ref
(
$feature
))
unless
check_ref
(
$feature
,
"
Bio::EnsEMBL::Transcript
");
my
$text_buffer
=
"";
#filehandle is inherited
my
$fh
=
$self
->
{'
filehandle
'};
print
$fh
$text_buffer
;
}
1
;
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