[ensembl-dev] Ensembl API 74: Fetch repeats identified by repeatmasker

[swaraj basu]

Dear All,

I want to fetch coordinates of repeat elements identified by the repeat
masker program in multiple species (BED format). I am using the following
code to get the desirable results

*my $slice = $slice_adaptor->fetch_by_region( $csn, $srn ); *#csn AND srn
ARE PREDEFINED BY ME












*my @repeats = @{ $slice->get_all_RepeatFeatures() };foreach my $repeat
(@repeats) {    my $id = $repeat->display_id();    my $start =
$repeat->start();    my $end = $repeat->end();    my $strand =
$repeat->strand();    my $score = $repeat->score();    my $name =
$csn.$srn;    my $analysis = $repeat->analysis();    my $program =
$analysis->program();    next unless $program eq "RepeatMasker";    print
"$name\t$start\t$end\t$id\t$score\t$strand\n";}*

My code is fetching me results for human, mouse, zebrafish, cavefish but
for *Tetraodon*, the $analysis->program() scalar remains undefined. Hence I
am unable to extract the RepeatMasker predictions on the *Tetraodon *genome.
Can someone please help.

-Regards

Swaraj Basu
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