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ensembl-gh-mirror
ensembl
Commits
35cb69eb
Commit
35cb69eb
authored
May 10, 2002
by
Arne Stabenau
Browse files
tested sequence getting for slices, seems to work correctly.
parent
80b45f89
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4 deletions
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-4
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+9
-4
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modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
View file @
35cb69eb
...
...
@@ -138,6 +138,10 @@ sub fetch_by_Slice_start_end_strand {
$self
->
throw
("
$slice
isn't a slice
");
}
if
(
$end
==
-
1
)
{
$end
=
$slice
->
chr_end
()
-
$slice
->
chr_start
()
+
1
;
}
$self
->
fetch_by_assembly_location
(
$slice
->
chr_start
()
+
$start
-
1
,
...
...
@@ -156,9 +160,10 @@ sub fetch_by_Slice_start_end_strand {
Arg 1 : int $chrStart
Arg 2 : int $chrEnd
Arg 3 : int $strand
Arg 3 : txt $chrName
Arg 4 : txt $assemblyType
Function : retrieve speciefied sequence from db. Using AssemblyMapper.
Arg 4 : txt $chrName
Arg 5 : txt $assemblyType
Function : retrieve specified sequence from db. Using AssemblyMapper. Gaps are
filled with N
Returntype: txt
Exceptions: Wrong parameters give undef as result
Caller : general, fetch_by_Slice_start_end_strand
...
...
@@ -174,7 +179,7 @@ sub fetch_by_assembly_location {
$mapper
->
register_region
(
$chrName
,
$chrStart
,
$chrEnd
);
my
@coord_list
=
$mapper
->
map_coordinates_to_rawcontig
(
$chrStart
,
$chrEnd
,
$chrName
,
$strand
);
(
$chrName
,
$chrStart
,
$chrEnd
,
$strand
);
# for each of the pieces get sequence
my
$seq
=
"";
...
...
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