Hi,
I tried the 'w' option, but it seems to be worth, since
I got the following message, and I have seen that some data had been
lost (e.g. hg18mm8rn41.idb 899 820 Ko => 0 Ko).
>>> msa = cnestedlist.NLMSA('hs18mm8rn4','w',genomeUnion)
>>> msa.build()
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "cnestedlist.pyx", line 2004, in pygr.cnestedlist.NLMSA.build
File "cnestedlist.pyx", line 1964, in
pygr.cnestedlist.NLMSA.buildFiles
pygr.nlmsa_utils.EmptyAlignmentError: empty alignment!
I have a safe copy of the data and if we consider that the program run
correctly up to the following command :
msa = cnestedlist.NLMSA('hs18mm8rn4','w',genomeUnion,glob.glob('./maf/
*'))
what I have to do now to use this NLMSA from inside pygr ?
Thanks
Michel
On May 25, 4:23 pm, Namshin Kim <deepr...@gmail.com> wrote:
> 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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