Public bug reported:
1) Ubuntu release: 18.04 LTS (Bionic Beaver)
2) Package versions: python-biopython 1.70+dfsg-4, python-biopython-sql
1.70+dfsg-4 (solves problem)
3) Expected: script that works elsewhere to work on bionic as well
4) What happened: script fails when python-biopython-sql is not installed,
with errors like
File "/usr/lib/python2.7/dist-packages/Bio/SeqRecord.py", line 440, in
__getitem__
from BioSQL.BioSeq import DBSeqRecord
ImportError: No module named BioSQL.BioSeq
5) Solution and analysis: The offending line (#440) reads
from BioSQL.BioSeq import DBSeqRecord
Installing python-biopython-sql solves the problem. It thus seems that
python-biopython should depend on python-biopython-sql. I notice that
python-biopython-sql does depend on python-biopython, so this would
introduce a mutual (circular) dependency. A solution to avoid having
mutually dependent packages might be to merge python-biopython-sql into
the main / base python-biopython package.
** Affects: python-biopython (Ubuntu)
Importance: Undecided
Status: New
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https://bugs.launchpad.net/bugs/1788632
Title:
dependency on python-biopython-sql missing
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