Hi,
First, I think you need to confirm whether you have all valid maf files in
your maf directory. Do not include starting with upstream... or something.
Second, instead of os.listdir, I suggest you use glob.glob. os.listdir does
not concatenate directory path, thus it may not give correct paths.
glob.glob('*.maf')
Namshin Kim
On Tue, May 19, 2009 at 7:36 PM, michel bellis <fill.i...@9online.fr> wrote:
>
> Hi,
>
> As I had memory problems when trying to construct a multialignment
> ressource on windows
> (see my post 'pb cnestedlist.NLMSA '), I shift to a linux platform
> (Scientific Linux SL release 5.0 (Boron) with python 2.4).
>
> If I start the cnestedlist.NLMSA command from inside the maf
> directory, the construction of
> built files runs correctly, but an error is raised when the idb file
> is processed as a MAF file :
>
> >>> os.chdir('./maf')
> >>> msa = cnestedlist.NLMSA('hs18mm8rn4','w',genomeUnion,os.listdir('./))
> ***
> *** WARNING: Unknown sequence bosTau2.scaffold27 ignored...
> *** WARNING: Unknown sequence canFam2.chr3 ignored...
> Processing MAF file: hs18mm8rn41.idb
> Traceback (most recent call last):
> File "<stdin>", line 1, in ?
> File "cnestedlist.pyx", line 1508, in
> pygr.cnestedlist.NLMSA.__init__
> File "cnestedlist.pyx", line 1752, in
> pygr.cnestedlist.NLMSA.readMAFfiles
> IOError: hs18mm8rn41.idb: not a MAF file? Bad format.
>
> If I start from inside the parent directory, maf files can't be
> accessed :
>
> >>> msa = cnestedlist.NLMSA('hs18mm8rn4','w',genomeUnion,os.listdir('maf'))
> Processing MAF file: chr2.maf
> Traceback (most recent call last):
> File "<stdin>", line 1, in ?
> File "cnestedlist.pyx", line 1508, in
> pygr.cnestedlist.NLMSA.__init__
> File "cnestedlist.pyx", line 1748, in
> pygr.cnestedlist.NLMSA.readMAFfiles
> IOError: unable to open file chr2.maf
>
> I had exactly the same access problem on windows.
>
> Thanks for your help
>
> Michel
> >
>
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