I would like to report a problem I encountered while using the Genbank to Five Column Format tool on the Galaxy Europe server.
The job failed with the following error message:
ImportError: cannot import name 'UnknownSeq' from 'Bio.Seq'
Based on the traceback, the tool appears to attempt importing the UnknownSeq class from Biopython, but this class is no longer available in the version currently installed on the server. This suggests a possible compatibility issue between the tool (cpt_gbk_to_5col) and the Biopython version in the Galaxy environment.
The relevant part of the traceback is:
File ".../BIO_FIX_TOPO.py", line 8, in record_end
from Bio.Seq import Seq, UnknownSeq
ImportError: cannot import name 'UnknownSeq' from 'Bio.Seq'
As far as I can tell, the error does not appear to be caused by the input GenBank file itself, but rather by a software dependency issue.
Could you please let me know whether this issue is already known and whether there are plans to update or fix the tool? If there is a recommended workaround or an alternative tool that provides equivalent functionality, I would be grateful for your advice.
