On May 12, 2009, at 3:08 AM, michel bellis wrote:
>
> Chris,
>
> The results I have sent are in order as I entered in the pydev console
> (eclipse on Windows XP). So the os.listdir is before construction of
> the NLMSA.
that's odd. Why would there be .idDict and .seqIDdict files *before*
building the NLMSA. I guess you already tried to build it before, and
these are left over from old builds.
>
>
> I tried your code and got a lot of file longer than 1 000 000. But I
> do not undestand what is the limit exactly.
The limit is that my brain was inoperative when I wrote that. I meant
1 billion, because I wanted it to report any sequence that might go
over the 32 bit int limit. But what's 3 orders of magnitude between
friends, anyway?
>
> I ran it with a different value (>= 2 000 000 000) and was surprised
> to find this:
> mm8.chrM 2666011489
>
> So I reconstructed mm8 without chrM. And then at the end I got this:
> mm8.chr9_random 2666012422 (which was hg18.chr9_random 1146434
OK, as I thought, something is going wrong with the reading of your
sequence file. Was chrM the *last* sequence in the file? And
chr9_random the next-to-last sequence? That would imply that the last
sequence length is always getting screwed up. Looking at the
seqfmt.pyx code, I don't see any obvious reason why that could occur.
Assuming that 'mm8' is the name of your fasta input file, try the
following test code:
from pygr import seqfmt
f = file('mm8')
d = {}
seqfmt.read_fasta_lengths(d, f, 'mm8')
print d # see if the sequence length is already crazy at this point
Finally, what platform (Windows via Cygwin?) and Python / Pyrex
versions are you using?
-- Chris
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