a ruby based version of kmer iterations and kmer graph preparation. It counts the kmers and gives the occurrences. An implementation of the exact match string algorithm. You can use this over the entire fasta by using the File.open(readlines). Saw this code kmercount so wrote this.
def kmers(sequence, kmer)
=BEGIN
#!/usr/bin/ruby
# Universitat Potsdam
# Date: 2024-3-15
# Author: Gaurav Sablok
=END
seqsplitter = sequence.split(//)
kmeriter = kmer.to_i
seqkmers = []
for i in 0..seqsplitter.length-kmeriter
seqkmers.push(seqsplitter.slice(i,i-i+kmeriter).join)
end
return seqkmers.each { | iter | puts iter.to_s + "\t" + seqkmers.count(iter).to_s }
end
# run like this and it will output the frequency tables.
kmers("AAGAAATGAGAAGTAATCAGAAAACCACTTAAGG", 31)
AAGAAATGAGAAGTAATCAGAAAACCACTTA 1
AGAAATGAGAAGTAATCAGAAAACCACTTAA 1
GAAATGAGAAGTAATCAGAAAACCACTTAAG 1
AAATGAGAAGTAATCAGAAAACCACTTAAGG 1
Gaurav
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany
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