On Fri, Jul 10, 2009 at 05:47:53PM -0700, Marek Szuba wrote: -> - the following, produced when cnestedlist.NLMSA objects are created -> (see e.g. tests/pairwise_hg18_megatest.py:103): -> -> " -> Note: the NLMSA.seqDict was not saved to a file. -> This is not necessary if you intend to save the NLMSA to worldbase. -> But if you wish to open this NLMSA independently of worldbase, -> you should call NLMSA.save_seq_dict() to save the seqDict info to a -> file, or in the future pass the saveSeqDict=True option to -> NLMSA.build(). -> -> To turn off this message, use the verbose=False option -> " -> -> It is the latter that has been giving me trouble - maybe I'm just very -> stupid today but I cannot figure out how to pass verbose=False or -> saveSeqDict=True to the function that triggers this warning, without -> modifying cnestedlist.pyx... The problem as I see it is as follows: -> -> - the warning is produced by NLMSA.buildFiles(), which recognises both -> saveSeqDict and verbose and sets them by default to False and True, -> respectively. This method in turn is called by NLMSA.build(), which -> doesn't recognise these options but both takes **kwargs and passes it -> to buildFiles(); -> -> - depending on the constructor's parameters, there are -> three ways NLMSA.build() can be called: -> NLMSA.__init__() -> NLMSA.readMAFfiles() -> NLMSA.build() -> NLMSA.__init__() -> NLMSA.readAxtNet() -> NLMSA.build() -> NLMSA.__init__() -> NLMSA.build() -> -> Then again, regardless of the scenario build() is *always* called with -> no parameters whatsoever! Therefore, unless I've missed something here, -> NLMSA.buildFiles() will always be called with its default values of -> saveSeqDict and verbose.
Just to make sure, you're talking about situations where 'build' isn't being called manually, right? Anytime you're constructing the NLMSA yourself you can call build with whatever you want. (It doesn't solve the megatest problem, but I wanted to clarify.) I'd be +1 for simply adding a few parameters to the constructor that are saved for later use by 'build' -- e.g. NLMSA(..., saveSeqDict=True) would set the default for buildFiles(). 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 -~----------~----~----~----~------~----~------~--~---
