Hi Brent, the problem is that you are querying specifically with the union_seq that you constructed afresh in this script, which did not come from pygr.Data. That's why it works when you use the msa constructed afresh from union_seq, but not when you use the msa from pygr.Data. The thing that obscured this was that the printing of the proper error message was screwed up by our recent seqdb_review. I fixed this in the latest master branch in the public repository.
The simple fix is to change is to change your line: for item, edge in msa[union_seq['sorghum.10'][1:40400]].items(): to for item, edge in msa[msa.seqDict['sorghum.10'][1:40400]].items(): In the case where msa was loaded from pygr.Data, msa.seqDict will be the object loaded from pygr.Data. In the case where msa was constructed afresh from union_seq etc., msa.seqDict will be union_seq (just as you assigned it). Does this make sense to you, or do you think that users will find this confusing? FYI, pygr.Data (and pygr in general) does not attempt to analyze whether different objects (created on different occasions potentially by different users) are actually the same underlying data. You might think that because you opened "the same file" on two occasions it should consider those two different objects to be equivalent. Of course, all sorts of things might have changed in between different file open operations, so the only reliable way to test equivalence would be to compute a md5 hash or equivalent on the complete data represented by that object. We've avoided such potentially performance-killing approaches in favor of the KISS approach of pygr.Data: if the user saved the object as name X, within a single interpreter session every request for name X is guaranteed to get the same object (unless you specifically turn off this behavior by using pygr.Data.clear_cache() to force future requests to reload...). Again, does this make sense to you, or do you think users will find this confusing? Thanks for reporting and analyzing this problem!!! -- Chris --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
