Hi everyone,
I'm trying to work with the ensembl perl api, but seem to be unable to do what I want. API -> http://www.ensembl.org/info/data/api.html
What I want is this:
I have a set of genomic positions from snp-calling. For each of the positions I want to know how conserved these single positions are compared to/in other species. So I figured I use the Compara API, which contains whole genome alignments, and some of the code here: http://www.ensembl.org/info/docs/api..._tutorial.html So basically I am looking for something like:
$bases_for_pos_1 = $alignment_human2mouse->getBases($human_position1)
$bases_for_pos_2 = $alignment_human2mouse->getBases($human_position2)
etc...(simplified, not real compara code)
The problem:
I can retrieve a 'GenomicAlignBlock' which contains the position I am looking for, but also a whole lot of surrounding sequence and I wander how I can get just the bases (from human and the other species) at the specific position...? Or even just whether they are equal or not.
Anyone?
-Stef
I'm trying to work with the ensembl perl api, but seem to be unable to do what I want. API -> http://www.ensembl.org/info/data/api.html
What I want is this:
I have a set of genomic positions from snp-calling. For each of the positions I want to know how conserved these single positions are compared to/in other species. So I figured I use the Compara API, which contains whole genome alignments, and some of the code here: http://www.ensembl.org/info/docs/api..._tutorial.html So basically I am looking for something like:
$bases_for_pos_1 = $alignment_human2mouse->getBases($human_position1)
$bases_for_pos_2 = $alignment_human2mouse->getBases($human_position2)
etc...(simplified, not real compara code)
The problem:
I can retrieve a 'GenomicAlignBlock' which contains the position I am looking for, but also a whole lot of surrounding sequence and I wander how I can get just the bases (from human and the other species) at the specific position...? Or even just whether they are equal or not.
Anyone?
-Stef
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