[BioPython] Syntax error while parsing Blast output

[Martin MOKREJŠ]

Hi,

Michiel De Hoon wrote:
>>> Interestingly, the code I presented was taken directly from the 
>>> BioPython cookbook (including the "while 1" bit).
>> So it is.  Michiel - do you fancy tweaking that section of the tutorial?
> 
> That part of the tutorial is in the section "Deprecated BLAST parsers", which
> will be removed once the plain-text Blast parser is removed from Biopython.
> The description of NCBIStandalone.blastall says
> 
> "This command will generate BLAST output in XML format, ..."
> 
> So this is being described correctly in the documentation.
> 
> Nevertheless, it may be a good idea to remove the plain text Blast parser
> completely from Biopython in the upcoming release (which will probably be
> done this week), to avoid further confusion.

although I understand your points, are you sure to REMOVE it? What if people
need to parse elsewhere generated, maybe even in the past generated BLAST
text outputs? If you wanted to say that you will REMOVE the text-based parser
because it won't be maintained anymore and probably be usable for one or two
NCBI BLAST version only, then it is probably more understandable. Otherwise
I guess more people move to bioperl. ;) BTW, what if some people have older
BLAST version generating broken XML file formats? Or have to parse such
old files again?

Martin