On Fri, May 29, 2009 at 01:53:38PM -0700, Christopher Lee wrote: -> > Second, I tried pulling BlastHitParser into BlastHitParser (which -> > parses -> > BLAST output) and BlastHitsToBlocksParser (which extracts ungapped -> > blocks for use in NLMSA construction). I think the result makes -> > sense. -> > Take a look: -> > -> > http://github.com/ctb/pygr/commit/a53f279b4f97fadcf54fa805c4e670cd09f5565e -> > -> > Branch 'ctb_blast' at git://github.com/ctb/pygr.git. -> > -> > Let me know what you think. -> -> In general I like the idea of breaking up "monolithic" classes into -> cleaner modules of function. In this case I don't think I have -> understood what your purpose was, and how this usefully subdivides the -> functionality. The docstrings for the split classes don't give much -> of an explanation. A few questions: -> -> - Are you trying to make BlastHitParser a base class that *must* be -> extended before it becomes useful? I don't understand the value of -> giving it a parse_file() method, but then making that method just -> yield self. At best this seems like an internal interface, not -> something you would expose to users. Can you explain what the usage -> case for BlastHitParser is?
Right now, BlastHitParser can't easily be used outside of the context of pygr because of the way BlastHitParser.parse_file mingles parsing logic (if self.is_valid_hit() etc.) with return results. This is a first attempt to pull those apart. I probably should have been more grandiose in my initial efforts; I'll rectify that immediately and give you something a bit nicer. -> - Regarding nomenclature, I prefer the simple and mathematically -> precise term "intervals" over the more ambiguous term "blocks". At -> first I misunderstood what you meant by "Parse blast records into -> ungapped blocks"; I would suggest instead "Parse blast hits into -> aligned intervals". *shrug* that's fine by me. 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 -~----------~----~----~----~------~----~------~--~---
