fixed Ensembl interface problem
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Christopher Lee
Jun 23, 2011, 2:26:51 PM6/23/11
to Pygr Development Group
Hi,
for those of you who may be trying to use the Ensembl interface included in Pygr 0.8.2, I just pushed a fix for a problem that 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.
for those of you who may be trying to use the Ensembl interface included in Pygr 0.8.2, I just pushed a fix for a problem that 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.
-- Chris
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