[ensembl-dev] slice edit based on variation

[Duarte Molha]

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
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