Welcome to PyKmers’s documentation!

Getting Started with PyKmers

Dependencies

PyKmers relies on pygfa library to load GFA files. You can build this library downloading the source code from this repository. In order to build and install pygfa, you need python3, pip3 and setuptools.

python setup.py bdist_wheel
pip install dist/pygfa*.whl

Build and Install PyKmers

Once pygfa is installed, you can build and install PyKmers from here.

python setup.py bdist_wheel
pip install dist/pykmers*.whl

pykmers package

Module contents

PyKmers Module

Collection of functions to extract k-mers from GFA file.

Copyright (C) 2019 by Alessio Zanga <alessio.zanga@outlook.it> Emanuele Cavenaghi <cavenaghi.emanuele@gmail.com>

pykmers.pykmers.com(base)

Return complement base of given base

Parameters:base – Input base
Returns:Complement base
pykmers.pykmers.get_kmers_from_file(file, kmer_length, sorted=False, debug=False)

Find all the kmers that corresponds at the given sequence

Parameters:
  • file – Input GFA file
  • kmer_length – Kmer length
  • sorted – True to sort the kmers in lexicographical order
  • debug – True to show debug info
Returns:

List of kmers
pykmers.pykmers.get_kmers_from_string(sequence, k)

Find all the kmers that corresponds at the given sequence

Parameters:
  • sequence – Sequence
  • k – Kmer length
Returns:

List of kmers
pykmers.pykmers.get_paths_from_graph(graph)

Find paths in graph from root to leaf

Parameters:graph – Graph
Returns:List of path in the graph
pykmers.pykmers.get_sequence_from_path(graph, path)

Find the sequence that corresponds to the path without consider the overlap

Parameters:
  • graph – Graph
  • path – Path
Returns:

Sequence that corresponds to the path
pykmers.pykmers.get_subgraphs_from_graph(graph)

Divide graph in connected components

Parameters:graph – Graph
Returns:List of subgraphs
pykmers.pykmers.load_graph_from_file(file)

Load a MultiGraph instance of Networkx from GFA file using pygfa library

Parameters:file – Input GFA file
Returns:MultiGraph instance
pykmers.pykmers.rev_and_com(sequence)

Return reverse and complement sequence of given sequence

Parameters:base – Input sequence
Returns:Reverse and complement sequence

Indices and tables