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phac-nml / mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
Apache License 2.0
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Minimum Biopython version? #134

Closed cmfield closed 1 year ago

cmfield commented 1 year ago

Running any part of mob-suite I get this error:

  File "/nfs/nas22/fs2201/biol_micro_unix_modules/modules/software/MOB-Suite/3.1.4-foss-2020b/bin/mob_init", line 5, in <module>
    from mob_suite.mob_init import main
  File "/nfs/nas22/fs2201/biol_micro_unix_modules/modules/software/MOB-Suite/3.1.4-foss-2020b/lib/python3.8/site-packages/mob_suite/mob_init.py", line 13, in <module>
    from mob_suite.utils import init_console_logger
  File "/nfs/nas22/fs2201/biol_micro_unix_modules/modules/software/MOB-Suite/3.1.4-foss-2020b/lib/python3.8/site-packages/mob_suite/utils.py", line 2, in <module>
    from Bio.SeqUtils import gc_fraction
ImportError: cannot import name 'gc_fraction' from 'Bio.SeqUtils' (/nfs/nas22/fs2201/biol_micro_unix_modules/modules/software/Biopython/1.78-foss-2020b/lib/python3.8/site-packages/Bio/SeqUtils/__init__.py)

I believe this is because gc_fraction wasn't introduced until Biopython 1.8? Certainly I can't find it in any earlier version.

uyghbo commented 1 year ago

I also encountered this problem.

jrober84 commented 1 year ago

The requirements have been updated to require >= biopython 1.8