Ah, excellent.  I'm glad there *is* a way to do this, even though
these alignments are reference-centric.

I saw NLMSA regions before, but unfortunately I haven't been able to
get it to work yet.    I had been using a mixture of local and XMLRPC
db's for hg18_multiz44way and regions() would always return an empty
list (some error message would be more helpful).

However, for mm9_multiz30way, perhaps there is some build issue.

genome = worldbase('Bio.Seq.Genome.MOUSE.mm9', download=True)
msa = worldbase('Bio.MSA.UCSC.mm9_multiz30way', download=True)
curRegion = genome['chr1'][3241792:3242792]
msa[curRegion].regions()

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call
last)

/home/wbiesing/<ipython console> in <module>()

/usr/local/lib/python2.6/dist-packages/pygr/cnestedlist.so in
pygr.cnestedlist.NLMSASlice.regions()

ValueError: no LPO in nlmsaSlice.seqBounds?  Debug!


I haven't tried this with any other MSA's (I can only fit so many
genomes on my paltry disk).  Perhaps I am on old code?

pygr.__version__
'0.8.1'

Could also be a mixture of DB types that's causing the error.  As you
saw in my code, I download the mouse genome first, then the MSA.  As a
result, the Mouse genome is a SequenceDB while the others are all
BlastDB's.

{'anoCar1': <BlastDB '/home/shared/pygrdata/genomes/anoCar1'>,
...
 'loxAfr1': <BlastDB '/home/shared/pygrdata/genomes/loxAfr1'>,
 'mm9': <SequenceFileDB '/home/shared/pygrdata/genomes/mm9'>,
 'monDom4': <BlastDB '/home/shared/pygrdata/genomes/monDom4'>,
...
 'tupBel1': <BlastDB '/home/shared/pygrdata/genomes/tupBel1'>,
 'xenTro2': <BlastDB '/home/shared/pygrdata/genomes/xenTro2'>}

Anything else I can provide to help track down the issue?

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