[bip] Blog post on bioinformatics and Python

[Peter]

Peter Clarke wrote:
>
> Ok, My euro's worth of random rant...
>
> I have been using biopython since 2000. I think there are a number of issues.
> ...
> I need parsers to be up to date. Updating of the biopython parser for
> 'normal' blast parsing was stopped without warning and so code failed
> to work without any notice of why.

I don't think that is really fair. Are you subscribed to the mailing
list?  There have been multiple discussions where people had trouble
parsing plain text output (usually due to a recent version of the NCBI
blast tools in combination with an older version of Biopython), where
the XML parser has been recommended.  In Biopython 1.44 (almost a year
ago), I even added a FAQ entry on this to the tutorial:

Question: Why doesn't Bio.Blast work with the latest plain text NCBI
blast output?
Answer:  The NCBI keep tweaking the plain text output from the BLAST
tools, and keeping our parser up to date is an ongoing struggle.  We
recommend you use the XML output instead, which is designed to be read
by a computer program.

May I ask if you reported a problem with the plain text parser at the
time (on the biopython mailing lists or bugzilla)?

> ... I think that unless Biopython adopts a strategy similar to this
> [fragmentation?] then it is going the way of Numerical python.

Going the way of numerical python would be an excellent outcome, given
how widely used both Numeric/numpy are :)

Peter (the one at Biopython)