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 > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
