Commit 65ce5d24 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Remove one instance of double 'my' in

_fetch_by_Slice_start_end_strand_circular().
parent 04bb67f9
......@@ -47,6 +47,7 @@ use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
use Bio::EnsEMBL::Utils::Cache;
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
......@@ -145,9 +146,19 @@ sub fetch_by_Slice_start_end_strand {
$start = 1 if(!defined($start));
$end = $slice->end() - $slice->start() + 1 if(!defined($end));
if ( !defined($end) ) {
$end = $slice->end() - $slice->start() + 1;
}
throw("Start must be less than or equal to end.") if($start > $end);
if ( $start > $end ) {
if ( $slice->is_circular() ) {
return
$self->_fetch_by_Slice_start_end_strand_circular( $slice,
$start, $end, $strand );
} else {
throw("Start must be less than or equal to end.");
}
}
$strand ||= 1;
......@@ -246,6 +257,148 @@ sub fetch_by_Slice_start_end_strand {
}
sub _fetch_by_Slice_start_end_strand_circular {
my ( $self, $slice, $start, $end, $strand ) = @_;
assert_ref( $slice, 'Bio::EnsEMBL::Slice' );
$strand ||= 1;
if ( !defined($start) ) {
$start ||= 1;
}
if ( !defined($end) ) {
$end = $slice->end() - $slice->start() + 1;
}
if ( $start > $end && $slice->is_circular() ) {
my $midpoint = $slice->seq_region_length - $slice->start + 1;
my $seq1 = ${
$self->_fetch_by_Slice_start_end_strand_circular( $slice, 1,
$midpoint, 1 )
};
my $seq2 = ${
$self->_fetch_by_Slice_start_end_strand_circular( $slice,
$midpoint + 1,
$slice->length(), 1 )
};
my $seq = $slice->strand > 0 ? "$seq1$seq2" : "$seq2$seq1";
reverse_comp( \$seq ) if ( $strand == -1 );
return \$seq;
}
# Get a new slice that spans the exact region to retrieve dna from
my $right_expand = $end - $slice->length(); #negative is fine
my $left_expand = 1 - $start; #negative is fine
if ( $right_expand || $left_expand ) {
$slice =
$slice->strand > 0
? $slice->expand( $left_expand, $right_expand )
: $slice->expand( $right_expand, $left_expand );
}
# Retrieve normalized 'non-symlinked' slices. This allows us to
# support haplotypes and PARs.
my $slice_adaptor = $slice->adaptor();
my @symproj =
@{ $slice_adaptor->fetch_normalized_slice_projection($slice) };
if ( @symproj == 0 ) {
throw( 'Could not retrieve normalized Slices. Database contains '
. 'incorrect assembly_exception information.' );
}
# Call this method again with any slices that were 'symlinked' to by
# this slice.
if ( @symproj != 1 || $symproj[0]->[2] != $slice ) {
my $seq;
foreach my $segment (@symproj) {
my $symlink_slice = $segment->[2];
# Get sequence from each symlinked area.
$seq .= ${
$self->fetch_by_Slice_start_end_strand( $symlink_slice, 1,
undef, 1 ) };
}
if ( $strand == -1 ) {
reverse_comp( \$seq );
}
return \$seq;
}
# We need to project this slice onto the sequence coordinate system
# even if the slice is in the same coord system, we want to trim out
# flanking gaps (if the slice is past the edges of the seqregion).
my $csa = $self->db->get_CoordSystemAdaptor();
my $seqlevel = $csa->fetch_sequence_level();
my @projection =
@{ $slice->project( $seqlevel->name(), $seqlevel->version() ) };
my $seq = '';
my $total = 0;
my $tmp_seq;
# Fetch sequence from each of the sequence regions projected onto.
foreach my $segment (@projection) {
my ( $start, $end, $seq_slice ) = @{$segment};
# Check for gaps between segments and pad them with Ns
my $gap = $start - $total - 1;
if ($gap) {
$seq .= 'N' x $gap;
}
my $seq_region_id = $slice_adaptor->get_seq_region_id($seq_slice);
$tmp_seq = ${
$self->_fetch_seq( $seq_region_id, $seq_slice->start(),
$seq_slice->length() ) };
# Reverse compliment on negatively oriented slices.
if ( $seq_slice->strand == -1 ) {
reverse_comp( \$tmp_seq );
}
$seq .= $tmp_seq;
$total = $end;
}
# Check for any remaining gaps at the end.
my $gap = $slice->length() - $total;
if ($gap) {
$seq .= 'N' x $gap;
}
# If the sequence is too short it is because we came in with a
# seqlevel slice that was partially off of the seq_region. Pad the
# end with Ns to make long enough
if ( length($seq) != $slice->length() ) {
$seq .= 'N' x ( $slice->length() - length($seq) );
}
if ( defined( $self->{_rna_edits_cache} )
&& defined(
$self->{_rna_edits_cache}->{ $slice->get_seq_region_id } ) )
{
$self->_rna_edit( $slice, \$seq );
}
return \$seq;
} ## end sub _fetch_by_Slice_start_end_strand_circular
sub _rna_edit {
my $self = shift;
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment