parsing blast xml to MSA/PSSM
what i want to do is run a blastp search on a protein sequence, then derive a PSSM from the results.
The embl-pi site has an api that allows me to run a blastp search programatically, however i can only get the results in the xml format, which turns out to be tedious to parse.
Biopython has BlastIO.blast_xml.BlastXmlParser, but i can not seem to figure out how to atleast get the pairwise alignments from that.
I appreciate any help
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