The cortexpy API reference

Random access of cortexpy graphs

This module contains classes for inspecting cortex graphs with random access to their kmers.

class cortexpy.graph.parser.random_access.RandomAccess(graph_handle, kmer_cache_size=None)

Provide fast k-mer access to Cortex graph in log(n) time (n = number of kmers in graph)

__getitem__(lexlo_string)

Return kmer associated with kmer string

No check is performed to make sure that the input string is a lexicographically-lowest kmer string. Use get_kmer_for_string() in order to convert a kmer string to its lexlo form before retrieving it from the cortex object.

__iter__()

Iterate over kmer strings in graph in order stored in graph

get_kmer_for_string(string)

Will compute the revcomp of kmer string before getting a kmer

items()

Iterate over kmer strings and kmers in graph in order stored in graph

values()

Iterate over kmers in cortex graph

Utility functions

This module contains utility functions that are used inside cortexpy. These functions may also be useful outside of cortexpy.

cortexpy.utils.kmerize_contig(contig, kmer_size)

Return generator of kmers in contig

The returned kmers are not lexicographically lowest.

>>> list(kmerize_contig('ATTT', 3))
['ATT', 'TTT']

cortexpy.utils.kmerize_fasta(fasta, kmer_size)

Return generator to all kmers in fasta

cortexpy.utils.lexlo

Return lexicographically lowest version of a kmer string and its reverse complement

The reverse complement of a kmer string is generated and the lexicographically-lowest kmer string is returned.

>>> lexlo('AAA')
'AAA'

>>> lexlo('TTT')
'AAA'