[Biopython-dev] New release

Peter biopython at maubp.freeserve.co.uk
Thu Jun 26 20:32:07 UTC 2008

On Thu, Jun 26, 2008 at 1:50 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Hi everybody,
> I think we should make a new Biopython release within the next couple of weeks
> to solve the issues with NCBI and to get the fixed Blast parser out (for output
> from Blast 2.2.18). There are a few outstanding issues that hopefully can be
> fixed before the next release:
> 1) NCBI access from Bio.GenBank
> 2) Bug #2454 (Iterators can't use file-like objects), which affects a number of parsers in Biopython
> 3) Martel-based parsers.

Given the updates to Bio.EUtils to enforce the 3 second rule, the
urgent part of issue (1) is now resolved, and any futher refinements
needn't hold up the release.

>From a technical viewpoint, none of these are very complicated. 2) is almost finished.

While there are still outstanding parsers affected by issue (2) (Bug
2454), I don't think this need hold up the release.

> With respect to 3), a small number of parsers in Biopython are based on
> Martel (none of the major ones as far as I can tell). For some of these
> parsers, it is not quite clear if they are still useful. For the remaining ones,
>  it would be nice if they could be rewritten without using Martel -- that would
> let us get rid of the dependency on mxTextTools.

Again, while removing the dependency on mxTextTools is a worthwhile
aim, I don't think this should hold up the release.

> Any other urgent issues that need to be resolved before a release?

There is an AlignInfo alphabet issue I'm currently working on, and
expect to have fixed tomorrow.


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