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Changes

v3.0.0

API-breaking changes:

  • The strand on which to look for a pattern in AvoidPattern and EnforcePatternOccurence is not given by the location (strand 1, -1, or strand 0 to look in both strands).
  • AvoidNonUniqueSegments renamed in UniquifyKmers
  • Complete rewrite of CodonOptimization, method names are now use_best_codon,

New features

  • Support for different genetic codes in EnforceTranslation.
  • Support for non-standard start codons in EnforceTranslation
  • New AvoidMatches specification based on Bowtie.
  • AvoidChanges and EnforceChanges can now tunable (EnforceChanges(60%), AvoidChanges(max_edits=2))
  • New SequencePattern MotifPssmPattern.

Misc.

  • Got rid of some tables like Genetic code, now taken from Biopython.
  • Complete code restructuring by cutting large files into smaller ones.

v2.0.0

  • problem.n_mutations became problem.mutations_per_iteration for clarity
  • 'harmonized' option in CodonOptimize() replaced by harmonized_frequencies for clarity