So, for the pygr 0.8 release, will the SQLTable and SQLGraph support the order of iteration? So that I can implement the one-to-many relationship between translation and exon properly, as discussed during the sprint session at Caltech.
What has also been discussed in the sprint session is to use standard pygr components for all sorts of mapping needed for ensembl features. The only case that a custom class is needed is when a joint of multiple tables is required. Currently, I wrote custom mapping classes for gene-transcript mapping and transcript-translation mapping. The one-to-many relationship between gene-transcript is provided in the transcript table. Likewise, the relationship between transcript-translation is provided in the translation table. Thus, I should not need to write mapping classes for them. Will current SQLGraph supports this kind of mapping? --jenny On Tue, Sep 9, 2008 at 12:31 PM, Christopher Lee <[EMAIL PROTECTED]> wrote: > > Hi All, > actually, I think Jenny is making a really important point: her > Ensembl functionality depends on 0.8 functionality that isn't released > yet, so announcing an "official release" of the ensembl functionality > now would be wishful thinking. To most people, an "official release" > means there's a *package* that *works* and is *supported*. > Unfortunately, that's not the situation here. My impression is that > Jenny's ensembl functionality won't work with any official Pygr > release (0.7.1 being the most recent). So we don't have a "package > that works". Jenny may have been planning on telling users that they > should get the latest Pygr source from git, but that is *not > supported*. So either way, this doesn't meet the criteria for a > release. > > To my mind this says Jenny should make her code available as a "pre- > alpha" version; this signals users to "try at your own risk" and "give > us feedback so we can make it better". That is the honest, > appropriate way to present this. > > By contrast, calling this an official release could lead to a lot of > confusion and questions from users. I'm already getting questions > about this e.g. today from EBI. On the one hand it's great to see > people are really interested in this. On the other hand, it worries > me. Nothing can be more disruptive to a proper release process than > making users angry that "the software doesn't work" by positioning > something as an *official release* when in reality it is pre-alpha. > > Yours, > > Chris > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
