[pygr-notify] Issue 97 in pygr: IOError: Iterator has no database

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Status: New
Owner: pygr-bug... at googlegroups.com
Labels: Type-Defect Priority-Medium

New issue 97 by kmdaily: IOError: Iterator has no database
http://code.google.com/p/pygr/issues/detail?id=97

What steps will reproduce the problem?
In [1]: from pygr import worldbase
In [2]: msa = worldbase("Bio.MSA.UCSC.dm3_multiz15way")
In [3]: genome = worldbase("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]

What is the expected output? What do you see instead?
I would expect a NLMSASlice, or a KeyError if it doesn't exist. Instead, an
IOError is raised:

---------------------------------------------------------------------------
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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