Hi,
I'm using phmmer search and I want to convert the output to XML, in order to have the percentage of identity parameter (which does not exist in any of the other formats, to the best of my knowledge). I've read about the package Hmmer.IO in Biopython, but didn't see an option to convert the output to XML. I've also read about Easel and esl-reformat command, but didn't find my desired option there either. Does anyone have a solution to this problem? My main goal is to extract the percentage of identity and coverage from Hmmer output, so if there's any other way to get these parameters besides the XML format, I'd love to hear about it.
Thank you!
if the identity parameter is already in the output, why do you need to convert to XML ?
I don't see the percentage of identity anywhere in my output file. Here's a part of it (I know it's a bit messy, but I didn't find a way to attach a file here)
so , converting this to XML won't change anything isn't it ?
Okay, so do you know how to get the identity percentage and coverage from Hmmer output, using python?
Biopython's
Bio.SearchIO
module currently only reads in various formats like HMMER or BLAST - it does not handle output.