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 On Thu, Sep 3, 2009 at 1:06 PM, Christopher Lee <l...@chem.ucla.edu> wrote: > > > On Sep 3, 2009, at 12:15 PM, Paul Rigor (gmail) wrote: > > > But don't I also have to build the individual genome resources as > > well? In any case, it would be great if the non-existent ponAbe2 > > genome would be made available through XMLRPC as well. > > I don't know what exactly your script tries to do, but download=True > mode is intended to be a one-step method of getting a target resource > and ALL its dependencies. That means if you request the 44 genome > alignment with download=True, it will automatically get the 44 genomes > also with download=True. In each case it will check your local > resources first; if you have a given resource locally already, of > course it will not be downloaded again. Note that you must have a > writable local metabase in your WORLDBASEPATH, so that it can > automatically save your downloaded resources to a local metabase for > future re-use (i.e. so that in the future it will know that the data > are available locally, and how to load them). > > The bottom line is: you just type > > msa = worldbase.Bio.MSA.UCSC.hg18_multiz44way(download=True) > > and it should do everything for you. If that is not working with this > specific resource, tell us, so that we can fix that. > > -- Chris > > > > -- Paul Rigor Graduate Student Institute for Genomics and Bioinformatics Donald Bren School of Information and Computer Sciences University of California, Irvine http://www.paulrigor.net/ http://www.ics.uci.edu/~prigor --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
