diff --git a/codonbias/__init__.py b/codonbias/__init__.py index affeeff..c8e603e 100644 --- a/codonbias/__init__.py +++ b/codonbias/__init__.py @@ -20,18 +20,25 @@ - Directional Codon Bias Score (DCBS) - Codon Usage Frequency Similarity (CUFS) -The package contains 4 submodules: +This package also includes tools for sequence optimization based on these +codon usage models, and generators of random sequence permutations that +can be used to compute empirical p-values and z-scores. + +The package contains 6 submodules: - codonbias.stats: Classes for basepair / codon statistics. - codonbias.scores: Models / scores that operate on individual sequences independently. - codonbias.pairwise: Models / scores that operate on pairs of sequences. -- codonbias.optimizers: Algorithms for score-based optimization of a sequence. +- codonbias.optimizers: Algorithms for score-based optimization of a + sequence. +- codonbias.random: Random sequence permutations for empirical z-scores + and p-values. - codonbias.utils: Helper functions for the other submodules. """ -__version__ = "0.2.0" +__version__ = "0.3.0" __author__ = 'Alon Diament' import codonbias.utils @@ -39,3 +46,4 @@ import codonbias.scores import codonbias.pairwise import codonbias.optimizers +import codonbias.random diff --git a/setup.py b/setup.py index d0706cb..3bc6141 100644 --- a/setup.py +++ b/setup.py @@ -16,6 +16,7 @@ install_requires=['numpy', 'scipy', 'pandas', + 'pandarallel' ], classifiers=[