kmers --- generate kmer frequency tables from text streams


author: Erik Garrison <erik.garrison@bc.edu>

license: MIT

usage: ./kmers [kmermin] [kmermax]
Generate kmer frequency statistics for all kmers in stdin between
kmermin and kmermax size.


overview:

We could generate statistics for all 4-mers in the string ATGCATGC using the
following invocation.

% echo ATGCATGC | tr -d '\n' | ./kmers 4 4
kmer    count   freq    lfreq
ATGC    2       0.4	    -0.39794
CATG    1       0.2	    -0.69897
GCAT    1       0.2	    -0.69897
TGCA    1       0.2	    -0.69897

Here count is the number of occurances, freq is the frequency of the kmer out
of all possible kmers in the input of that length (e.g. here there are 5
possible kmers of length 4 in a string of 8 characters), and lfreq is
log10(freq).

This program can be used to generate kmer frequency information for standard
FASTA reference files as follows:

% cat reference.fasta \
    | sed "/^>.*$/d" \  # delete sequence names
    | tr -d '\n' \      # remove newlines
    | ./kmers 1 11 \    # generate kmer frequency information from 1bp to 11bp
    | grep -v N \       # remove kmers containing "N"s
    >reference.kmers.tsv

Note that memory usage could be extremely high with longer kmers, in the order
of kmer length * input size for each kmer length between kmermin and kmermax.