On Wed, Jun 24, 2009 at 12:05:29AM -0400, [email protected] wrote: -> I completed my first draft of interfacing clustalw and blastz to pygr. Here is the like to the source code -> http://github.com/eloseden/pygr-align/tree/master.? Comments are wel-come.
Hi Eden, thanks for sending this out! My usual collection of misc comments follows... For the Clustalw stuff, - the MAF stuff isn't being used any more, I believe; you should probably remove all of the references to it, as well as the write_MAF function. - isn't the genomes_dict stuff completely unnecessary in setUp? - please put spaces after comment marks, '# comment', as per PEP 8 ;) - ClustalwResiduess should inherit from 'object'; - Some of your line lengths are > 80; please put in line breaks! The only place where this is sort of OK is where you have long filenames on the line. - I would suggest having create_NLMSA_clustalw take a file object rather than a filename, as the first argument. - Again, in this function, the use of genomes_dict is unnecessary! The blastz tests are failing for me on lyorn; could you take a look why? cheers, --titus -- C. Titus Brown, [email protected] --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
