How to parse NCBI Blast XML to retrieve "hsp_query-from in Biopython?
Hey,
I have a question concerning parsng NCBI BLAST XML outputs. I can parse the hsp score of the BLAST results. Unfortunately, I face difficulties parsing other entries in the XML.
I need to parse hsp_query-from, hsp_query-to, hsp_align-len, and hsp_identity.
This code works:
for record in NCBIXML.parse(result_handle):
for alignment in record.alignments:
for hsp in alignment.hsps:
hsp_score = hsp.score
How can I get the other entries? Especially hsp_query-from seems to be tricky because "from" is reserved by python.
I appreciate your help a lot!
Best, Philipp
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1 answer
- hsp_query-from: hsp.query_start
- hsp_query-to: hsp.query_end
- hsp_align-len: hsp.align_length
- hsp_identity: hsp.identities
You can lookup the keywords in the source code of the NCBIXML parser at http://biopython.org/DIST/docs/api/Bio.Blast.NCBIXML-pysrc.html to find the respective parameters.
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