[Biopython] parsing hmmer results

[Wibowo Arindrarto]

Hi Michael,

Do you have an example file you can send over (sending it to me
privately also works). The parser has not been tested with HMMER
version 3.1, and I suppose they introduced some changes which breaks
the parser.

Best,
Bow

On Tue, Mar 11, 2014 at 1:43 PM, Michael Thon <mike.thon at gmail.com> wrote:
> 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
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