Hi Paul, Yes, it should also get all dependencies with download=True. How this is supposed to work: When a resource is saved to worldbase, its dependencies should also have worldbase IDs. I.e. in the case of the 44 genome alignment, its seqDict (a PrefixUnionDict) contains references to each of the 44 genomes. When the alignment is pickled by worldbase, that will automatically recurse to pickle the dependencies, including each of the 44 genomes. Those genomes should each be marked with its worldbase ID; in that case pickling simply saves the worldbase ID rather than including the pickle of the genome in the pickle of the alignment. When Pygr unpickles the alignment, it simply launches new worldbase requests for these IDs, in order to get them. If the alignment was requested with download=True, the new requests will also be requested with download=True.
When the alignment was first saved to worldbase, its genomes will be marked with their worldbase IDs if either - those genomes were themselves obtained from worldbase; - or those genomes were saved to worldbase in this commit or a previous commit. If a genome did not have a worldbase ID when the alignment was saved to worldbase, worldbase obviously cannot just save the genome as its worldbase ID, but instead must include its pickle in the alignment pickle. In that case it will be retrieved along with the alignment, but it cannot be saved to worldbase locally (again because it has no ID). That could conceivably lead to the situation you are seeing (where only the alignment is stored in your local metabase). -- Chris On Sep 3, 2009, at 1:21 PM, Paul Rigor (gmail) wrote: > No genomes were listed once I downloaded the 44way alignment. > Here's an ipython session > > In [1]: from pygr import worldbase > > In [2]: worldbase.dir() > Out[2]: > ['0root', > '0version', > 'Bio.MSA.UCSC.hg18_multiz44way', > 'Bio.MSA.UCSC.hg18_multiz44way.txt', > '__doc__.Bio.MSA.UCSC.hg18_multiz44way', > '__doc__.Bio.MSA.UCSC.hg18_multiz44way.txt'] > > > From my understanding, the multiple alignment is generated from MAF > files and the coordinates are mapped to existing genome resources. > So you're saying that with this single MSA download step, all of the > necessary genomes will also be downloaded? > > 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 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 -~----------~----~----~----~------~----~------~--~---
