v0.3.1

Full Changelog: 0.3.0...v0.3.1

v0.3.0

• new:
  • new module: optimizers with the classes MaxWeight, MinWeight, and BalancedWeight
  • new module: random with the classes Permuter, IntraSeqPermuter and IntraPosPermuter
  • added utils.ReferenceSelector
• changed:
  • utils.translate returns a dataframe by default
• fixed:
  • avoid numpy deprecation warning in VectorScore's get_vector function

Full Changelog: 0.2.0...0.3.0

v0.2.0

• new:
  • added scores.NormalizedTranslationalEfficiency
  • added scores.CodonPairBias
  • added stats.BaseCounter for nucleotide and k-mer statistics across reading frames
  • added k_mer parameter to:
    • stats.CodonCounter
    • scores.CodonAdaptationIndex
    • scores.EffectiveNumberOfCodons
    • pairwise.CodonUsageFrequency
  • added abstract class scores.WeightScore that computes a weight vector for each input sequence, with the following children:
    • scores.CodonPairBias
    • scores.EffectiveNumberOfCodons
    • scores.RelativeSynonymousCodonUsage
    • scores.RelativeCodonBiasScore
• improved:
  • various improvements to scores.EffectiveNumberOfCodons
    • background correction
    • improved estimation
  • added count() method to counter classes
  • added pseudocount parameter to models

Full Changelog: 0.1.0...0.2.0

v0.1.0

First release.

• stats.CodonCounter
• scores.FrequencyOfOptimalCodons (FOP)
• scores.RelativeSynonymousCodonUsage (RSCU)
• scores.CodonAdaptationIndex (CAI)
• scores.EffectiveNumberOfCodons (ENC)
• scores.TrnaAdaptationIndex (tAI)
• scores.RelativeCodonBiasScore (RCBS + DCBS)
• pairwise.CodonUsageFrequency (CUFS)