Hi Chris, 

We are still having trouble with the MSA. We were able to build it without 
any errors using pygr/0.8.2

However when we try to load and query it, we get the following error. 

In [1]: from pygr import worldbase

In [2]: genome = worldbase.Bio.Seq.Genome.MOUSE.mm10()

In [3]: msa = worldbase.Bio.Seq.Alignments.MOUSE.mm10.multiz60way()

In [4]: slice = genome['chrY']

In [5]: res = msa[slice]
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-5-628143efd160> in <module>()
----> 1 res = msa[slice]

pygr/msa-builder/build/lib.linux-x86_64-2.6/pygr/cnestedlist.so in 
pygr.cnestedlist.NLMSA.__getitem__()

pygr/msa-builder/build/lib.linux-x86_64-2.6/pygr/cnestedlist.so in 
pygr.cnestedlist.NLMSASlice.__cinit__()

AttributeError: 'pygr.cnestedlist.NLMSA' object has no attribute 'doSlice'

Any clue? 

Vishal



On Thursday, April 25, 2013 10:23:33 AM UTC-7, Vishal Patel wrote:
>
> Hi, 
>
> We usually download the pygr NLMSA from the UCLA server. However, the 
> latest mm10 - multiz60way alignment does not exist there so we decided to 
> build it. 
>
> First I ran into issues with max size, 
>
> *       1 msa = cnestedlist.NLMSA(pathstem=pathstem,*
> *       2                             seqDict=genomeUnion,*
> *----> 3                             mafFiles=maflist, mode="w")*
> *
> *
> *site-packages/pygr-0.8.2-py2.7-linux-x86_64.egg/pygr/cnestedlist.so in 
> pygr.cnestedlist.NLMSA.__init__()*
> *site-packages/pygr-0.8.2-py2.7-linux-x86_64.egg/pygr/cnestedlist.so in 
> pygr.cnestedlist.NLMSA.readMAFfiles()
> *
> *
> *
> *ValueError: MAF block too long!  Increase max size*
>
> Setting the maxlen and maxint to a billion also did not help so I set it 
> to sys.maxint. 
>
> However this code still fails because it open 1000's of ".build" files and 
> fails because it does not have "write permission" on the next file handle 
> it tries to open. Basically hits the max open files limit. I increased the 
> ulimit to 10,000 files at which point it fails with "Segmentation fault 
> (core dumped)"
>
> Here is lsof out every 0.1 s when it failed, 
> 170 # these are file handles to genome files
> 170
> 170
> 170
> 170
> 170
> 170
> 726 # starts creating .build files
> 1682
> 2443
> 3706
> 6300
> 7209
> 9160 # hits the upper limit again and fails with a core dump. 
>
> I have tried this with py2.6/pygr0.8.1 and py2.7/pygr0.8.2 and get the 
> same error. 
>
> Has anyone experienced this? 
> What are the .build files?
>
> Vishal
>
>
>
>
>
>
>
>
>

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