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AvoidPattern with biopython FeatureLocation raises AttributeError (in some specific parameters)

See original GitHub issue

Adding a simple DNA pattern TGAA as an AvoidPattern constraint causes an AttributeError, the stack trace is listed below

"/usr/local/lib/python3.8/site-packages/dnachisel/DnaOptimizationProblem/mixins/ConstraintsSolverMixin.py", line 357, in resolve_constraints
    self.resolve_constraint(constraint=constraint)
  File "/usr/local/lib/python3.8/site-packages/dnachisel/DnaOptimizationProblem/mixins/ConstraintsSolverMixin.py", line 251, in resolve_constraint
    evaluation = this_local_constraint.evaluate(self)
AttributeError: 'NoneType' object has no attribute 'evaluate'

Issue Analytics

State:
Created 3 years ago
Comments:11 (9 by maintainers)

Top GitHub Comments

1reaction

Zulkocommented, Mar 30, 2021

I have to admit I have no clue what Biopython version supports what values 😦 . I think replacing None strands by 0 should be pretty safe (someone will scream if it isn’t 😄 )

1reaction

veghpcommented, Mar 30, 2021

Thanks for pointing out the problem; I’ll have to look into it to keep Biopython support for older version (as did with DNAalphabet). Alternatively we can drop support (?)

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