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ensembl-gh-mirror
ensembl
Commits
005f2dee
Commit
005f2dee
authored
9 years ago
by
ChuangKee Ong
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To use infor from provider meta key to update annotation source
parent
6a32827f
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2 merge requests
!104
To use dbprimary_acc instead of display_id;Fix GO source duplication
,
!104
To use dbprimary_acc instead of display_id;Fix GO source duplication
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1
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1 changed file
modules/Bio/EnsEMBL/Utils/SeqDumper.pm
+26
-3
26 additions, 3 deletions
modules/Bio/EnsEMBL/Utils/SeqDumper.pm
with
26 additions
and
3 deletions
modules/Bio/EnsEMBL/Utils/SeqDumper.pm
+
26
−
3
View file @
005f2dee
...
...
@@ -76,8 +76,8 @@ my $DUMP_HANDLERS =
'
GENBANK
'
=>
\
&dump_genbank
};
my
@COMMENTS
=
('
This sequence was annotated by
the Ensembl system
. Please visit
'
.
'
the Ensembl web site, http://www.ensembl.org/ or http://www.ensemblgenomes.org/ for more information.
',
('
This sequence was annotated by
###SOURCE###
. Please visit
'
.
'
the Ensembl
or EnsemblGenomes
web site, http://www.ensembl.org/ or http://www.ensemblgenomes.org/ for more information.
',
'
All feature locations are relative to the first (5
\'
) base
'
.
'
of the sequence in this file. The sequence presented is
'
.
...
...
@@ -473,11 +473,22 @@ sub dump_embl {
$self
->
print
(
$FH
,
"
XX
\n
"
);
#References (we are not dumping refereneces)
#Database References (we are not dumping these)
#Get annotation source
my
(
$provider_name
)
=
@
{
$meta_container
->
list_value_by_key
('
provider.name
')};
my
(
$provider_url
)
=
@
{
$meta_container
->
list_value_by_key
('
provider.url
')};
my
$annotation_source
=
q{}
;
if
(
$provider_name
)
{
$annotation_source
.=
$provider_name
;
$annotation_source
.=
sprintf
(
q{(%s)}
,
$provider_url
)
if
$provider_url
;
}
else
{
$annotation_source
.=
'
Ensembl
';
}
#comments
foreach
my
$comment
(
@COMMENTS
)
{
$comment
=~
s/\#\#\#SOURCE\#\#\#/$annotation_source/
;
$self
->
write
(
$FH
,
$EMBL_HEADER
,
'
CC
',
$comment
);
$self
->
print
(
$FH
,
"
XX
\n
"
);
}
...
...
@@ -656,8 +667,20 @@ sub dump_genbank {
#refereneces
#Get annotation source
my
(
$provider_name
)
=
@
{
$meta_container
->
list_value_by_key
('
provider.name
')};
my
(
$provider_url
)
=
@
{
$meta_container
->
list_value_by_key
('
provider.url
')};
my
$annotation_source
=
q{}
;
if
(
$provider_name
)
{
$annotation_source
.=
$provider_name
;
$annotation_source
.=
sprintf
(
q{(%s)}
,
$provider_url
)
if
$provider_url
;
}
else
{
$annotation_source
.=
'
Ensembl
';
}
#comments
foreach
my
$comment
(
@COMMENTS
)
{
$comment
=~
s/\#\#\#SOURCE\#\#\#/$annotation_source/
;
$self
->
write
(
$FH
,
$GENBANK_HEADER
,
'
COMMENT
',
$comment
);
}
...
...
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