Error with Fetch Taxonomic Representation

Hello everyone,

I am trying to fetch taxonomic data from my Blast results. I have chosen to include the Taxonomic data columns when running Blast on my data. And when trying to choose the GI column to show taxonomic representation for, the column with the taxon ID did not appear as an option to choose. There are 39 columns in my Blast file but only 29 columns appeared as options that can be chosen.

So instead of Taxon ID, I chose Subject GI column as the GI column to run Fetch Taxonomic Representation. However, the job resulted in an error stated below.

File “/opt/galaxy/shed_tools/”, line 36

  • except Exception, e:
  •                ^

SyntaxError: invalid syntax

So I am not sure how to go about running this tool in this case. If anyone has experienced similar issue, some help on how to resolve this would be greatly appreciated.

Update: The pull request has been accepted and should be available on the usegalaxy servers shortly.


Thanks for the bug report, the problem was that the gi2taxonomy tool was written before python 3 was released, when the syntax except Exception, e: was supported. In python 3, that syntax was no longer supported, being replaced with except Exception as e:

I’ve created a pull request to update the tool to be compatible with the new syntax, and you can follow the progress here