On May 11, 2009, at 9:28 AM, michel bellis wrote:
> msa = cnestedlist.NLMSA('hs18mm8rn4','w',genomeUnion,os.listdir
> ('maf'))
>
> Traceback (most recent call last):
> File "<console>", line 1, in <module>
> File "cnestedlist.pyx", line 1508, in
> pygr.cnestedlist.NLMSA.__init__
> File "cnestedlist.pyx", line 1735, in
> pygr.cnestedlist.NLMSA.readMAFfiles
> OverflowError: long int too large to convert to int
Hi Michel,
this is odd -- it is claiming that an individual sequence in your
union of hg18, mm8 or rn4 is longer than 2GB. Maybe something was
wrong with the reading of the sequence files (e.g. an incompatible
carriage return mode?), so that it read an entire genome file as one
sequence? Could you try the following:
for name,info in genomeUnion.seqInfoDict.iteritems():
if info.length > 1000000:
print name,info.length
Also, is your os.listdir() output from *before* or *after* trying to
construct the NLMSA from maf files?
-- Chris
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