[ensembl-dev] slice edit based on variation

Duarte Molha duartemolha at gmail.com
Tue Mar 6 15:41:48 GMT 2018


Hi Anja

Your code does something akin to what I was already doing. I just wanted to
make sure there wasn't a more straightforward way to tackle this problem/

Many thanks

Duarte




[image: --]
Duarte Molha
[image: https://]about.me/duarte
<https://about.me/duarte?promo=email_sig>

On 6 March 2018 at 09:31, Anja Thormann <anja at ebi.ac.uk> wrote:

> Hi Duarte,
>
> we do have code that deals with a slightly different version of your use
> case. The code
> <https://github.com/Ensembl/ensembl-variation/blob/release/91/modules/Bio/EnsEMBL/Variation/TranscriptHaplotypeContainer.pm#L1157-L1160> we
> have constructs transcript haplotypes from phased variants. You could take
> a look and see if you could extract some of the code for your use case. But
> at the moment I cannot point you to any API function that could help you
> with your use case.
>
> Kind regards,
> Anja
>
> On 5 Mar 2018, at 14:49, Duarte Molha <duartemolha at gmail.com> wrote:
>
> Hi guys
>
> I was wondering if I could get some pointers from you about the best way
> to accomplish a task.
>
> I have a genomic slice and an array of variations features that overlap
> that slice
>
> Is there a elegant way of modifying the slice sequence to incorporate one
> or more of the alternative alleles of each variant without doing a bunch of
> substring concatenations?
>
> for example for the sake of simplicity I have a 10 bp slice sequence on
> chr1:100-110 bp
>
> AATTAGTATG
>
> and I have a known variant at position 102 A/T
>
> my required outcome would be
>
> A*[T]*TTAGTATG =>  ATTTAGTATG
>
> Ideally I would like to use the Perl api where possible and be able to
> generalise this process as best as possible so that i can input a variable
> number of variants of different types
> For example, say that on the same 10 bp sequence I had 2 variations and
> one was a 1bp deletion:
>
> AATTAGTATG
>
> var 1 pos 102 [A/T]
> var2  pos 106 [G/-]
>
> the output would be
>
> A[*T]*TTA[-]TATG  =>  A*T*TTATATG
>
> Any suggestions?
>
> Many thanks
>
> Duarte
> _______________________________________________
> 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/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20180306/2c79afd3/attachment.html>


More information about the Dev mailing list