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). The new filters are: OLD ---> NEW: read_aligned_coords ---> CoordsToIntervals generate_tblastn_intervals ---> TblastnTransform (part of read_aligned_intervals) ---> save_aligned_intervals read_aligned_intervals ---> renamed to read_blast_intervals read_blast_intervals now takes a pipeline argument, which is just a list of filter functions to apply instead of save_aligned_intervals -- simple and flexible. blastx_results no longer takes any arguments except the input of aligned intervals. add_aligned_intervals() no longer takes any arguments except the input of aligned intervals. This completely cleaned up (got rid of) all the kwargs passing you disliked. I also followed your suggestions for cleaning up the AttributeInterface stuff further. 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 -- Chris --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
