Export Frequency Counts

This section describes how to export frequency counts of k-mers.

import oxli
kmer_table3 = oxli.KmerCountTable(ksize=3)

# Count some k-mers
kmer_table3.consume('AAAAA') # 'AAA' x 3
kmer_table3.count('TTT') # 'AAA' + 1
kmer_table3.count('AAC') # count 1

# Export (frequency,count) tuples
kmer_table3.histo(zero=False) # [(1, 1), (4, 1)]

# Include frequencies with 0 counts
kmer_table3.histo(zero=True) # [(0, 0), (1, 1), (2, 0), (3, 0), (4, 1)]

Convert frequency count list into a Pandas dataframe.

import pandas as pd
histo_output = kmer_table3.histo(zero=True)

# Create a Pandas DataFrame from the list of tuples
df = pd.DataFrame(histo_output, columns=['Frequency', 'Count'])

print(df)

   Frequency  Count
0          0      0
1          1      1
2          2      0
3          3      0
4          4      1