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.
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