So I'm having what I think is a similar issue with some local data. We have the alignment + genomes from Bio.MSA.UCSC.dm3_multiz15way built locally. When I set my WORLDBASEPATH to only look locally, I try the same code:
In [3]: msa = worldbase.Bio.MSA.UCSC.dm3_multiz15way() In [4]: triCas2 = worldbase.Bio.Seq.Genome.TRICA.triCas2() In [5]: seq = triCas2['singleUn_263'][2437:2453] In [6]: msa[seq] --------------------------------------------------------------------------- IOError Traceback (most recent call last) /home/baldig/projects/genomics/nonsvn/output/fly/motifsearch/ 2009_7_30_13_19_39_3_211_1/<ipython console> in <module>() /home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/ python2.6/site-packages/pygr-0.8.0-py2.6-linux-x86_64.egg/pygr/ cnestedlist.so in pygr.cnestedlist.NLMSA.__getitem__() /home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/ python2.6/site-packages/pygr-0.8.0-py2.6-linux-x86_64.egg/pygr/ cnestedlist.so in pygr.cnestedlist.NLMSASlice.__cinit__() /home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/ python2.6/site-packages/pygr-0.8.0-py2.6-linux-x86_64.egg/pygr/ cnestedlist.so in pygr.cnestedlist.IntervalFileDBIterator.loadAll() /home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/ python2.6/site-packages/pygr-0.8.0-py2.6-linux-x86_64.egg/pygr/ cnestedlist.so in pygr.cnestedlist.IntervalFileDBIterator.nextBlock() IOError: Iterator has no database! Please provide a db argument. How long ago was the bug squashed? I thought we were running on a fairly recent version of pygr... Would it be enough to update to the latest version of pygr or should I rebuild the resources? Thanks again! On Aug 4, 7:07 pm, jbiesinger <[email protected]> wrote: > fixedforme. Thanks a ton for the quick response! > > On Aug 4, 6:25 pm, Namshin Kim <[email protected]> wrote: > > > Hi, > > I had updated pygr using latest version as of today and restarted the XMLRPC > > server. Please check it again. > > > Yours, > > Namshin Kim > > > On Wed, Aug 5, 2009 at 10:19 AM, Christopher Lee <[email protected]> wrote: > > > > Hi, > > > it turns out the XMLRPC server is running an old version of Pygr that > > > had a bug in reloading of NLMSAs. That was fixed about two months > > > ago, but the server is running an older version. We will restart the > > > XMLRPC server with the 0.8 beta version. > > > > Thanks for reporting this!!! > > > > -- 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 -~----------~----~----~----~------~----~------~--~---
