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

[swaraj basu]

Thanks for the useful information.


On Thu, Feb 20, 2014 at 5:13 PM, mag <mr6 at ebi.ac.uk> wrote:

>  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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-- 
Swaraj Basu
PhD Student (Bioinformatics - Functional Genomics)
Animal Physiology and Evolution
Stazione Zoologica Anton Dohrn
Naples
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