pykmers package¶

Module contents¶

PyKmers Module

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

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