On Sun, Jun 07, 2009 at 10:07:27PM -0700, C. Titus Brown wrote: -> On Sun, Jun 07, 2009 at 10:04:24PM -0700, C. Titus Brown wrote: -> -> -> -> On Wed, Jun 03, 2009 at 10:06:32PM -0700, Christopher Lee wrote: -> -> -> On Jun 1, 2009, at 9:58 PM, C. Titus Brown wrote: -> -> -> -> -> -> > blastx_database - allow blastx/tblastx to be run on databases -> -> -> > -> -> -> > blastx_generator - return blastx results via generator -> -> -> > -> -> -> > ctb_intervals - refactoring & commenting of NLMSA -> -> -> > add_aligned_intervals code -> -> -> -> -> -> Hi Titus, -> -> -> I merged and extended these branches in a new branch, -> -> -> intervals_filter. This extends the refactoring that you did, to make -> -> -> all of the functions in this process into real "filters" (i.e. a -> -> -> generator function that takes a single argument as its input, and -> -> -> returns an iterator suitable for use as input to the next filter). -> -> -> -> [ ... ] -> -> -> -> -> -> -> Please take a look at this branch (uploaded to github) and let me know -> -> -> what you think: -> -> -> http://github.com/cjlee112/pygr/tree/interval_filters -> -> -> -> Wow, that's a lot of refactoring in blast.py! -> -> -> -> I fixed some docstrings and places where the line lengths went over 80 -> -> chars; see my 'interval_filters' changes here, -> -> -> -> http://github.com/ctb/pygr/tree/interval_filters -> -> Err, I forgot to say: I like the changes a lot! I think the code ends up -> being even simpler and more general.
...and here are some more patches to blast.py, downstream of my interval_filters patches: http://github.com/ctb/pygr/tree/more_blast_patches minor updates to blast.py: make explicit __call__ in __getitem__, fix __repr__ in subclasses, remove unusable **kwargs The only change that might be controversial is the removal of **kwargs from __getitem__; you can't use kwargs with the [] call to __getitem__, so I thought they should be removed from the __getitem__ function definition. (I'm working on the doc_alignments branch and happened to run across these things.) cheers, --titus -- C. Titus Brown, c...@msu.edu --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
