Hi,
I had did it :
msa = cnestedlist.NLMSA('hs18mm8rn4','r',genomeUnion)
msa.build()
Traceback (most recent call last):
File "<console>", line 1, in <module>
File "cnestedlist.pyx", line 1992, in pygr.cnestedlist.NLMSA.build
ValueError: not opened in write mode
Michel
On 25 mai, 13:21, Namshin Kim <deepr...@gmail.com> wrote:
> Hi,
> If you didn't save seqDict, you have to supply seqDict just like when you
> created NLMSA (change 'w' into 'r' this time).
>
> msa.build()
> msa.save_seq_dict()
>
> Yours,
> Namshin Kim
>
> On Mon, May 25, 2009 at 6:25 PM, michel bellis <fill.i...@9online.fr> wrote:
>
> > Hi,
>
> > I have constructed NLMSA files on a Linux station with success, but
> > the last step failed.
> > I checked the folder and file access mode, and have not seen anything
> > abnormal. I transfered the data on a Windows station where I obtained
> > the same error message.
>
> > Thanks for your help,
>
> > Michel
>
> > *** WARNING: Unknown sequence oryCun1.scaffold_208340 ignored...
> > *** WARNING: Unknown sequence panTro1.chr6_random ignored...
> > warning: non-alignment text lines ignored: prefix
> > , count 16190860
> > warning: non-alignment text lines ignored: prefix #, count 48
> > Index files saved.
> > Note: the NLMSA.seqDict was not saved to a file.
> > This is not necessary if you intend to save the NLMSA to pygr.Data.
> > But if you wish to open this NLMSA independently of pygr.Data,
> > you should call NLMSA.save_seq_dict() to save the seqDict info to a
> > file,
> > or in the future pass the saveSeqDict=True option to NLMSA.build().
>
> > To turn off this message, use the verbose=False option
>
> > >>> msa.build(saveSeqDict=True)
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in ?
> > File "cnestedlist.pyx", line 1992, in pygr.cnestedlist.NLMSA.build
> > ValueError: not opened in write mode
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