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

[mag]

Hi Swaraj,

Unfortunately, the 'software' column for tetraodon is not populated.

If you want a more reliable way of finding repeats from repeatmasker, I 
would recommend using the analysis logic name ($analysis->logic_name)
That field is compulsory and any repeat mask based analysis will be 
named 'repeatmask%'


Hope that helps,
Magali

On 20/02/2014 15:53, swaraj basu wrote:
> 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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