[Biopython] Problems parsing with PSIBlastParser

[Miguel Ortiz Lombardia]

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