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Return subseq from correct side of seq when on reverse strand using a… #454

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Return subseq from correct side of seq when on reverse strand using a… #454

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4d71194
Return subseq from correct side of seq when on reverse strand using a…
aparton Sep 13, 2019
5933790
Call the strand in the right place
aparton Sep 13, 2019
c7dc1eb
Add test for slices on reverse strand
aparton Sep 13, 2019
f68290d
Use correct coordinates when falling back to database for patch sequence
aparton Feb 20, 2020
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20 changes: 16 additions & 4 deletions modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -360,10 +360,22 @@ sub _new_slice_seq {
return sub {
my ($self, $start, $end, $strand, $preserve_masking) = @_;
my ($seq, $length) = ('', 0);

$start = $start ? ($self->start + $start) - 1 : $self->start;
$end = $end ? ($self->start + $end) - 1 : $self->end;

my $orig_start = $start;
my $orig_end = $end;

$strand = defined($strand) ? $strand * $self->strand : $self->strand;

if($self->strand == 1) {
$start = $start ? ($self->start + $start) - 1 : $self->start;
$end = $end ? ($self->start + $end) - 1 : $self->end;
}
else{
my $input_end = $end;
$end = $end ? ($self->end - $start) + 1 : $self->end;
$start = $start ? ($self->end - $input_end) + 1 : $self->start;
}

my $sr_name = $self->seq_region_name;

# indels
Expand Down Expand Up @@ -396,7 +408,7 @@ sub _new_slice_seq {
print STDERR "USING DATABASE\n" if $DEBUG;
return
scalar(@_) > 1 ?
$self->_fasta_old_db_subseq($start, $end, $strand) :
$self->_fasta_old_db_subseq($orig_start, $orig_end, $strand) :
$self->_fasta_old_db_seq();
}
}
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8 changes: 8 additions & 0 deletions modules/t/fastaSequence.t
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Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,14 @@ is($slice1->subseq(3, 5, -1), 'CCA', 'subseq rev');
is($slice1->subseq(5, 4), '', 'subseq e > s');
is($slice1->subseq(-1, 5), 'CGCATGG', "subseq overlap 5'");

# test subseq on transcript feature slice on reverse strand
my $stable_id = 'ENST00000346798';
my $transcript_adaptor = $cdb->get_TranscriptAdaptor();
my $transcript = $transcript_adaptor->fetch_by_stable_id($stable_id);
my $transcript_slice = $transcript->feature_Slice;
is($transcript_slice->subseq(1, 2), 'CA', 'subseq on slice on reverse strand');



# test going off ends
$slice1 = $sa->fetch_by_region('chromosome', 21, 1, 10);
Expand Down