[Biopython] parsing hmmer results

[Michael Thon]

I’m trying to parse a batch hmmer v3.1b1 report but I keep getting this error.  I think its happening when the parser hits a hmmer report with no hits, but I’m not sure.

Here’s the error:

Traceback (most recent call last):
  File "parse-dbcan.py", line 6, in <module>
    for qresult in SearchIO.parse(argv[1], 'hmmer3-text'):
  File "/Library/Python/2.7/site-packages/Bio/SearchIO/__init__.py", line 316, in parse
    for qresult in generator:
  File "/Library/Python/2.7/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py", line 47, in __iter__
    for qresult in self._parse_qresult():
  File "/Library/Python/2.7/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py", line 109, in _parse_qresult
    qid = regx.group(1).strip()
AttributeError: 'NoneType' object has no attribute ‘group'


Here’s my script:

#!/usr/bin/python
from Bio import SearchIO
from sys import argv
import pdb

for qresult in SearchIO.parse(argv[1], 'hmmer3-text'):
    hits = qresult.hits
    if len(hits) > 0:
        beste = hits[0].hsps[0].evalue
        query = hits[0].query_id
        hit = hits[0].id.replace('.hmm', '')
        print query + ',' + hit + ',' + str(beste)
        #pdb.set_trace()

I ran hmmscan like this:

hmmscan --cpu 2  -E 1e-3 HMMs.txt prots.fasta >oute-3.txt