biopythonでHMMERの結果をparseする

まずはHMMERで検索

hmmscan -o out_hmmscan.txt --cpu 4 -E 1e-10 prof.hmm some_proteins.fa

検索結果をparse

parse_hmmscan.py

# !/usr/bin/env python3

from Bio import SearchIO

qres=SearchIO.parse('out_hmmscan.txt', 'hmmer3-text') 

for q in qres:
    if len(q) >= 1:
        for hit in q:
            print('*** HIT ***')
            print(q.id)
            print(hit.id)
            print(hit.evalue)
            print()
            for hsp in hit:
                print(hsp.query.seq)
                print(str(hsp.aln_annotation['PP']))
                print(hsp.hit.seq)
                print()
            print()

環境

Ubuntu 18.04
hmmer 3.1b2
Python 3.7.2
biopython 1.72