v0.3.5

• improved: input type validation

Full Changelog: v0.3.4...v0.3.5

v0.3.4

• added: FrequencyOfOptimalCodons: weights arg (closes #5)
• fixed: pandas v2 compatibility (closes #5)
• improved: FrequencyOfOptimalCodons: default thresh 0.95 -> 0.8

Full Changelog: v0.3.3...v0.3.4

v0.3.3

What's Changed

• Use np.prod instead of np.product by @l-benedetti-insta in #4

New Contributors

• @l-benedetti-insta made their first contribution in #4

Full Changelog: v0.3.2...v0.3.3

v0.3.2

What's Changed

• tAI fixes/improvements by @moritzburghardt in #3
  • new: optimize_s_values method
  • new: allow custom s_values
  • fixed: handle invalid literal for int in gtrnadb table
  • fixed: CERTIFICATE_VERIFY_FAILED error on GtRNAdb

New Contributors

• @moritzburghardt made their first contribution in #3

Full Changelog: v0.3.1...v0.3.2

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)