thinking hard... the problem I reported is probably a network connection bug between the mysql client installed on my laptop and the Ensembl mysql public server. It has nothing to do with Pygr.
Since if you run the Python Ensembl API with the default PYGRDATAPATH setting, most of the Ensembl-related resources will be saved either to your home directory or to your current directory. Later on, when object-oriented code is executed, such as obtaining all the transcripts for a given gene (transcripts = gene.transcripts), related pygr.Data resources from your local directory will be called and sql queries will be constructed to retrieve the specific data by connecting to the Ensembl mysql public server. Sorry for the confusion. The only resources the Python Ensembl API users need to retrieve from the UCLA server are the genome assemblies. I am still not clear how the UCLA server returns a real genome build given a resource id? Jenny On Thu, Oct 23, 2008 at 9:19 AM, Christopher Lee <[EMAIL PROTECTED]> wrote: > > I don't think we even have a publicly accessible MySQL server, so I > don't know what you're referring to. Could you identify the specific > pygr.Data resource name that you're having this problem with, and > exactly how you request it? > > Namshin, am I right in thinking no UCLA external pygr.Data resources > should reference a UCLA external MySQL database server? > > -- Chris > > > On Oct 23, 2008, at 12:25 AM, Jenny Qing Qian wrote: > > > um... > > > > What's the version of the mysql server on your end? The version of > > mysql client installed on my computer is 5.0.51. The 'MySQL > > connection' bug has been reported to occur when a 5.0.51 client or > > lower tries to talk to a 5.0.52 server. > > > > Also, does the computer hosting the UCLA server have a 64-bit > > processor? My laptop only has a 32-bit processor. 'A 32-bit > > processor talks to a 64-bit processor' could also be the cause of > > the problem. > > > > jenny > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
