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? -- You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-...@googlegroups.com. To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en.