I have been using blast+ with the xml output format (-m7 in the older days, and outfmt 5 with ncbi-blast+). Since the XML files are huge, I have been gzipping them. I have also been using Biopython to parse the XML files. Is there a way to handle the gzipped file directly in (Bio)python?
gunzip output.xml.gzand use something like:
from Bio.Blast import NCBIXML blast_file = open ('output.xml') blast_records = NCBIXML.parse(blast_file)