Re: bioperl module to extract specific nucleotides given chromosome and exact location of that nucleotide

[biohisham]

So you basically have some coordinates and want to check if anyone of the alleles matches the location given by the coordinates right ? But your coordinates don't tell about which chromosome these alleles are expected but what you can probably do is download the chromosomes in say FastA format and then use Bio::SeqIO using the subseq function.

here is the documentation to the module Bio::SeqIO

The subseq function requires a beginning and an end to what it is going to extract so probably you want to reformat your coordinates as follows

$seq->subseq(coordinate-1, coordinate+1)

to extract three bases with the middle one being the actual nucleotide you want to compare your alleles against.

Note that BioPerl can be a bit slow and therefore consider using something like sfetch or esl-sfetch which will again require providing beginning and end positions to what it is to extract

[xxArwaxx]

I'll try this out and see! Still, more suggestions are welcomed! I was searching earlier and was able to find something that has to do with exact location being a method for a 'SeqFeature' object, and didn't have anything to do with chromosome number. I'm interested in finding allele1 and allele2 for that position.