[Biopython] Problems parsing with PSIBlastParser
Miguel Ortiz Lombardia
ibdeno at gmail.com
Wed Oct 14 12:49:30 UTC 2009
Le 14 oct. 09 à 14:37, Peter a écrit :
> On Wed, Oct 14, 2009 at 12:30 PM, Miguel Ortiz Lombardia
> <miguel.ortiz-lombardia at afmb.univ-mrs.fr> wrote:
>>
>> Hi again, Peter.
>>
>> Well, it turned out that I don't have such work-around... When I
>> launched
>> the script as:
>>
>> nohup lpbl.py ... &
>>
>> against all my sequences it choked at the first one (quite longer
>> than the
>> one I was using as an example) with the very same error.
>
> It would take longer as it would wait for BLAST to finish before
> starting
> to parse it.
>
>> However, this time I have the "temp.txt" file and indeed there
>> lines such as:
>>
>> Query: 0 -
>>
>> Sbjct: 445
>> G 445
>>
>> Query: 0
>>
>> Sbjct: 445
>> G 445
>>
>> Query: 0 ------
>>
>> Sbjct: 1316 ETNAPV
>> 1321
>>
>> present for some alignments and it cannot be parsed by my code.
>
> Those do look strange.
>
>> When I run blastpgp myself on the command line, same arguments, and
>> catch
>> the standard output to a temp2.txt file, the latter file does not
>> contain
>> those lines and can be parsed correctly.
>
> This is odd, and I am not sure what would cause this.
>
>> So, in the end I went back to my code and modified according to your
>> recommendation of using the commandline applications. The relevant
>> part of
>> code now looks like this:
>> ...
>> And it works!
>
> Great - I'm glad my vague instructions made sense :)
>
They were quite clear :-) and the pointer to the alignment tutorial
helped a lot.
>> Thanks again for your help,
>
> At least we have solution, even if we didn't get to the bottom of
> the strange BLAST output. I'll close the bug...
>
That's fine.
Thanks!
-- Miguel
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