[ensembl-dev] Ensembl API 74: Fetch repeats identified by repeatmasker
swaraj basu
projectbasu at gmail.com
Thu Feb 20 16:58:55 GMT 2014
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
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
--
Swaraj Basu
PhD Student (Bioinformatics - Functional Genomics)
Animal Physiology and Evolution
Stazione Zoologica Anton Dohrn
Naples
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140220/e5934deb/attachment.html>
More information about the Dev
mailing list