[Biopython-dev] New release

Michiel de Hoon mjldehoon at yahoo.com
Thu Jun 26 12:50:10 UTC 2008

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.

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

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



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