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

[D. Bradley]

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)