Can Biopython Parse Gzipped Xml From Blast?
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?
Presently, I
gunzip output.xml.gzand use something like:
from Bio.Blast import NCBIXML
blast_file = open ('output.xml')
blast_records = NCBIXML.parse(blast_file)
Thanks!
1 answer
Using the gzip module:
import gzip
from Bio.Blast import NCBIXML
blast_file = gzip.open('output.xml.gz', 'rb')
blast_records = NCBIXML.parse(blast_file)
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Jeroen Van Goey
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