[Biopython-dev] blastpgp parsing buglet

[Jeffrey Chang]

Great patch!  I've committed it.

Thanks,
Jeff


On Thursday, May 8, 2003, at 11:45  AM, Coleman, Michael wrote:

> Parsing by NCBIStandalone.py fails for BLASTP 2.2.5 output.  This is 
> the partial output that trips the problem:
>
> gi|23099742|ref|NP_693208.1| ornithine aminotransferase [Oceanob...   
> 430   e-119
> gi|16081241|ref|NP_393547.1| L-2, 4-diaminobutyrate:2-ketoglutar...   
> 430   e-119
>
> Sequences not found previously or not previously below threshold:
>
>> gi|23466947|gb|ZP_00122533.1| hypothetical protein [Haemophilus 
>> somnus 129PT]
>           Length = 432
>
>  Score =  591 bits (1524), Expect = e-167
>  Identities = 191/420 (45%), Positives = 291/420 (69%), Gaps = 7/420 
> (1%)
>
> The code expects to see a 'CONVERGED' but none is given here.  One 
> possible fix would be to also look for a line beginning with '>', like 
> so
>
>             # Read the descriptions and the following blank lines.
>             read_and_call_while(uhandle, consumer.noevent, blank=1)
>             l = safe_peekline(uhandle)
>             if l[:9] != 'CONVERGED' and l[:1] != '>':
>                 read_and_call_until(uhandle, consumer.description, 
> blank=1)
>                 read_and_call_while(uhandle, consumer.noevent, blank=1)
>
> Mike
>
> Mike Coleman, Scientific Programmer, +1 816 926 4419
> Stowers Institute for Biomedical Research
> 1000 E. 50th St., Kansas City, MO  64110
>
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