Python Library to compute and plot phylogeny Kmer signatures


License
MIT
Install
pip install kython==1.4.0

Documentation

Kython

Kmer Computation tools python library

This package was developped for a university project at Sorbonne université for the use of Kmer signatures in phylogenetic studies.

Installation:

pip3 install kython

Functions available:

  • Module pp:

      * DownloadSequences(Bacteria list file, Archaea list file, output path)-Download sequences From ncbi and returns a dictionnary of file paths
      * ParseSequences(path)--------------------------------------------------Retrieve the file path dictionnary from an existing folder
      * KmerSignature(path,kmer size,normalization) --------------------------Compute Kmer signature from a genomic .fna file path (use the dictionnary)
      * DistanceMatrix(dictGeneral:dict, kmer:int,phylum:str=None)------------Compute distance matrices from a dictionnary (phylum can be specified, default is all phylums combined)
      * NeighbourJoining(distance Matrix)-------------------------------------Compute Phylogenetic tree in Newick format from distance Matrix (using Neigbour Joining algorithm)
      * SequenceHomogeneity(path, kmer size, Genomic fragment size)-----------Compute Homgeneiy of sub sequences in the main sequence (using chisquare) and return list of intervals and p-values
    
  • Module pl:

      * KmerSignature(signature,organism name)--------------------------------Plots a signature in radial coordinates
      * SequenceHomogeneity(listPvalues,listPositions,pValue,organism,kmer)---Plots the sequence homogeneity
      * GraphTree(tree in newick format,DictGeneral,outputpath)---------------Plots a tree from a Newick tree structure