[ensembl-dev] odd results from getting variation features
Andrea Edwards
edwardsa at cs.man.ac.uk
Tue Dec 28 15:41:47 GMT 2010
Hi
Please see some code below to get watson snps. I am getting subslices of
each chromosome and then getting the watson snps (variation features)
for each slice. The variation features are sorted into order
The first subslice is bases 1 - 10,000 and contains no variation features
The second subslice is bases 10,001 - 20,000 and contains variants at
these positions
904
1081
4626
How can this be? I have pasted more output below to show further
subslices contain variation features not within the subslice range
thanks a lot
===========================================================
my @unsorted_slices = @{ $slice_adaptor->fetch_all('chromosome', undef,
0, 1) };
my @sorted_slices = sort by_num_then_letter @unsorted_slices;
# Base pair overlap between returned slices
my $overlap = 0;
# Maximum size of returned slices
my $max_size = 10000;
my @sub_slices = @{split_Slices( \@sorted_slices, $max_size, $overlap ) };
my $snp_id = 0;
foreach my $slice (@sub_slices) {
print "subslice start: ", $slice->start, " end: ", $slice->end, "\n";
unless ($slice->seq_region_name() =~ /Un/) {
my @vfs
=@{$watson_set->get_all_VariationFeatures_by_Slice($slice)};
my @sorted_vfs = sort { $a->start() <=> $b->start() } @vfs;
foreach my $vf (@sorted_vfs){
print vf->start();
}
}
=======================================================
subslice start: 1 end: 10000
subslice start: 10001 end: 20000
904
1081
4626
subslice start: 20001 end: 30000
547
600
620
subslice start: 30001 end: 40000
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