[Biopython-dev] Dropping the plain text BLAST parser?, was: Jython 2.7b2

[Fields, Christopher J]

On May 7, 2014, at 1:43 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, May 7, 2014 at 6:53 PM, Fields, Christopher J
> <cjfields at illinois.edu> wrote:
>> On May 7, 2014, at 12:21 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>> 
>>> Does anyone fancy that fairly boring task? We'd like to get
>>> rid of the NCBI plain text BLAST parser at some point - but
>>> anecdotally people continue to use it.
>> 
>> Just as an aside re: the pain of plain-text parsing: if you need an
>> extra data point, this is the same problem we’ve had with bioperl’s
>> (patched-to-death) BLAST parser.
>> 
>> chris
> 
> Hi Chris - I agree :)
> 
> It has been an effort over the years, but we have deprecated
> this code - the question is when to finally kill it... and how much
> outcry might there be?
> 
> Is BioPerl's plain text BLAST parser also on death row?

It might be best described as ‘needing to be euthanized’.  We don’t actively support it but ‘patches are welcome’ (e.g. we don’t actively fix bugs for it).

> Personally I think the NCBI has now improved the tabular/CSV
> output enough with BLAST+ that there is now no reason to use
> the plain text output.
> 
> I mean here that previously for some fields you had to use plain
> text, XML (or ASN.1) because the tabular output was lacking:
> http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions.html
> http://blastedbio.blogspot.co.uk/2014/02/blast-xml-output-needs-more-love-from.html
> 
> Regards,
> 
> Peter

Yes, agreed.  The problem (at least then) was that the majority of users then were users who wanted something to parse their (already-generated and possibly old) text output.  Hopefully that has changed somewhat.

chris