Hi Paul, one amendment to my previous answer: I suggest adding one argument to the build() call:
msa.build(saveSeqDict=True) # BUILD & SAVE ALIGNMENT + SEQUENCE INDEXES This tells it to save information about what sequence databases are aligned in msa, so that re-opening msa in a subsequent Python session will also attempt to reopen the correct sequence database(s) automatically. This is useful mainly if you plan on re-opening the msa manually; pygr.Data automatically forces this information to be saved / reloaded even if the msa was built without this argument. -- Chris On Dec 21, 2008, at 1:04 PM, Paul Rigor wrote: > > Hi, > > What is the best strategy for pickling pygr blast results? I receive > the following error when pickling a python dictionary containing the > result objects. > > File "pygr.cnestedlist.pyx", line 1660, in > pygr.cnestedlist.NLMSA.__iadd__ > File "/home/dock/shared_libraries/lx64/pkgs/python/2.5.1/lib/ > python2.5/site-packages/pygr/nlmsa_utils.py", line 97, in saveSeq > File "pygr.cnestedlist.pyx", line 1423, in > pygr.cnestedlist.NLMSASequence.__iadd__ > AttributeError: 'int' object has no attribute 'pathForward' > > > Thanks, > Paul > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
