Codon-Bias documentation

This Python package provides codon usage bias (CUB) analysis tools for genomic sequences, focusing on protein coding regions, translation efficiency and synonymous mutations.

Contents

• Getting started
  • Load sequences
  • Initialize a codon bias model
  • Compute gene scores
  • Compute positional weights
• codonbias package
  • Submodules
  • codonbias.optimizers module
    • BalancedWeight
      • BalancedWeight.optimize()
    • MaxWeight
      • MaxWeight.optimize()
    • MinWeight
      • MinWeight.optimize()
    • WeightOptimizer
      • WeightOptimizer.optimize()
  • codonbias.pairwise module
    • CodonUsageFrequency
    • PairwiseScore
      • PairwiseScore.get_matrix()
      • PairwiseScore.get_score()
  • codonbias.random module
    • IntraPosPermuter
    • IntraSeqPermuter
    • Permuter
      • Permuter.get_permuted_seq()
      • Permuter.get_pval()
      • Permuter.get_zscore()
  • codonbias.scores module
    • CodonAdaptationIndex
    • CodonPairBias
    • EffectiveNumberOfCodons
    • FrequencyOfOptimalCodons
    • NormalizedTranslationalEfficiency
    • RelativeCodonBiasScore
    • RelativeSynonymousCodonUsage
    • ScalarScore
      • ScalarScore.get_score()
    • TrnaAdaptationIndex
    • VectorScore
      • VectorScore.get_vector()
    • WeightScore
      • WeightScore.get_weights()
  • codonbias.stats module
    • BaseCounter
      • BaseCounter.count()
      • BaseCounter.get_table()
    • CodonCounter
      • CodonCounter.count()
      • CodonCounter.get_aa_table()
      • CodonCounter.get_codon_table()
  • codonbias.utils module
    • ReferenceSelector
      • ReferenceSelector.get_top_indices()
      • ReferenceSelector.get_top_seqs()
    • fetch_GCN_from_GtRNAdb()
    • geomean()
    • greater_equal()
    • less_equal()
    • mean()
    • process_GtRNAdb_table()
    • rankdata()
    • reverse_complement()
    • translate()

Indices and tables

• Index

• Module Index

• Search Page