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:
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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
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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