[BioPython] Syntax error while parsing Blast output

[Chris Fields]

On Oct 24, 2007, at 3:22 AM, Peter wrote:

> [Sorry you got this twice Michiel, I forgot to set the from/to fields]
>
>> 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.
>> ...
>> 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.
>
> Removing it sounds too drastic - especially as we have had people on
> the mailing list using it  deliberately fairly recently.  If you  
> really do want
> to remove this code, then adding a deprecation warning to the plain  
> text
> parser for the next release would be a more gentle route.
>
> I think there is still some benefit in having the plain text  
> parser, and that
> it could be fixed to cope with current multi-query files without  
> too much
> pain.  Maybe I should try this weekend...
>
> Anyone want to voice their opinion?
>
> Peter

We have a similar issue with the bioperl parsers.  We basically  
promote the BLAST XML parser over the text parser, but we have  
retained both due to demand.  In fact, we have two text parsers, a  
pull and a push parser (we're gluttons for punishment).  As for  
maintenance, we never guarantee how long it will take to fix text  
parsing if it breaks as the text format is fairly unstable by NCBI's  
own admission.

Our deprecation cycle is usually: (1) announce it on list to get  
feedback, (2) if deprecation is planned, add warnings to the module  
in the next release, (3) remove completely in a later release.  It  
gives everyone time to change over.

chris