Getting Started

This page provides a quick guide to getting started with the Oxli Python API.

Initialise a new KmerCountTable

# Import oxli
from oxli import KmerCountTable

# Create new count table
kct = KmerCountTable(ksize=4) # Count 4-mers

Adding k-mer counts.

# Add single k-mer with count()
kct.count("AAAA")
>>> 1

# Increment count
kct.count("AAAA")
>>> 2

# Forward and Reverse complement counted together
kct.count("TTTT")
>>> 3

# Add many k-mers from a longer sequence with consume
kct.consume("GGGGGGGGGG") # 7 x 4-mers of 'GGGG'

Lookup counts by k-mer.

# Retrieve kmer counts
kct.get('GGGG') # Count for GGGG/CCCC
>>> 7
kct.get('AAAA') #Count for AAAA/TTTT
>>> 3

Extracting k-mers from files.

# Screed for FASTA/FASTQ parsing
import screed

# Create new table
counts = KmerCountTable(ksize=21)

# Read fasta records and extract k-mers
for record in screed.open('doc/example.fa'):
    counts.consume(record.sequence)
>>> 349910