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

[Peter Cock]

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?

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