[pygr-notify] Issue 134 in pygr: UCSCEnsemblInterface fails with Genome doesn't exist error

[pygr at googlecode.com]

Status: FixedNeedsReview
Owner: pygr-bug... at googlegroups.com
Labels: Type-Defect Priority-Critical

New issue 134 by cjlee... at gmail.com: UCSCEnsemblInterface fails with Genome  
doesn't exist error
http://code.google.com/p/pygr/issues/detail?id=134

What steps will reproduce the problem?
1. create a UCSCEnsemblInterface object following the steps in the Ensembl  
interface tutorial

What is the expected output? What do you see instead?

Instead of getting an interface object, it raises an exception,
"Genome hg18 doesn't exist or has got no Ensembl data at UCSC"

This problem recently arose due to changes in UCSC's database.  The 0.8.2  
code assumed that a given UCSC dataset identifier (e.g. "hg18") would be  
associated with only a single row in the trackVersion table, but recently  
UCSC added multiple such rows.  This caused the pygr 0.8.2 code to fail  
when attempting to look up the right identifier for linking a UCSC dataset  
to a specific Ensembl dataset, reporting an error message like "Genome hg18  
doesn't exist or has got no Ensembl data at UCSC".  My fix simply tries  
each of the rows associated with the specified UCSC dataset, until it  
successfully makes a connection to an Ensembl dataset.  This fix will not  
affect anything outside of the Ensembl interface, and passes all our  
Ensembl + other tests.  I pushed this to the master branch on github for  
anyone who needs this prior to a next release of Pygr.