[Biopython] Parsing text output of hmmsearch from HMMER 3.1b1

[Wibowo Arindrarto]

Hi Bradley,

Thanks for reporting the bug. I can tell you that support for hmmer 3b1 is
not fully tested yet, so some output files may produce the output / error
you are seeing.

Would you mind sending the file as well (privately to me is also fine,
though I prefer public)?

Best regards,
Bow

On Fri, Jun 12, 2015, 17:56 D. Bradley <db534 at cam.ac.uk> wrote:

> Hello,
>
> I am trying to parse a text output file from HMMER vesion 3.1b1; the
> file was produced using the following command:
>
> * hmmsearch Pkinase.hmm H_sapiens.fasta.gz > PKhits.out
>
> In BioPython, I have tried to begin parsing this file by issuing the
> following commands:
>
> * from Bio import SearchIO
> * hmmer_qresult = SearchIO.read('PKhits.out', 'hmmer3-text')
>
> However, an error is produced and I get the following output:
>
> "qid = regx.group(1).strip()"
> "AttributeError: 'NoneType' object has no attribute 'group'"
>
>
> I do not know what the problem is. I am a beginner bioinformatician and
> this is actually the first time I've tried to parse anything, so maybe
> the error is simply in my understanding. However, from a quick web
> search, somebody else seems to have had a similar problem
> (http://permalink.gmane.org/gmane.comp.python.bio.general/8027).
>
> Any help would be greatly appreciated; I can send my output file
> straight away upon request.
>
> Best regards,
>
> David Bradley (PhD student)
>
>
>
>
>
>
>
>
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