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

Peter Cock p.j.a.cock at googlemail.com
Wed May 7 18:43:01 UTC 2014

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:



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