Sorry, just created an issue on the google code page. http://code.google.com/p/pygr/issues/detail?id=97
On Jun 8, 3:18 pm, Kenny Daily <[email protected]> wrote: > Any idea how/what this error means, or how one would get it? Using a > different sequence slice on the same chromome works fine. These > datasets are built directly from the UCLA biodb server. Thanks! > > In [1]: import pygr.Data > In [2]: msa = pygr.Data.getResource("Bio.MSA.UCSC.dm3_multiz15way") > In [3]: genome = pygr.Data.getResource("Bio.Seq.Genome.DROME.dm3") > In [4]: seq = -genome['chr3L'][10959977:10959996] > In [5]: seq > Out[5]: -chr3L[10959977:10959996] > > In [6]: print seq > ------> print(seq) > CATCCTGGTGACCCTGCTT > > In [7]: msa[seq] > --------------------------------------------------------------------------- > IOError Traceback (most recent call > last) > > /home/baldig/projects/genomics/nonsvn/output/fly/motifsearch/ > 2009_6_4_10_47_13_3_155_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. --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
