Commit 35cb69eb authored by Arne Stabenau's avatar Arne Stabenau
Browse files

tested sequence getting for slices, seems to work correctly.

parent 80b45f89
......@@ -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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