Oops. In read mode, do not build. That's is a normal behavior.
msa = cnestedlist.NLMSA('hs18mm8rn4','r',genomeUnion)
msa.save_seq_dict()
On Mon, May 25, 2009 at 11:19 PM, michel bellis <fill.i...@9online.fr>wrote:
>
> 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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