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#!/usr/bin/env python3
''' Some helpful utility functions.'''
def rev_comp(kmer):
''' Gets rev. comp of a k-mer.'''
res = ""
mapping = {
'A': 'T',
'C': 'G',
'G': 'C',
'T': 'A'
}
for i in range(0, len(kmer)):
res += mapping[kmer[-i - 1]]
return res
def get_minimizer_no_canonical(kmer, minimizer_len):
''' Get no canonical minimizer of a k-mer.'''
minimizer = kmer[0:minimizer_len]
for i in range(1, len(kmer) - minimizer_len + 1):
candidate = kmer[i:minimizer_len+i]
if candidate < minimizer:
minimizer = candidate
return minimizer
def get_minimizer(kmer, minimizer_len):
''' Get canonical minimizer of a k-mer.'''
rev = rev_comp(kmer)
candidate1 = get_minimizer_no_canonical(kmer, minimizer_len)
candidate2 = get_minimizer_no_canonical(rev, minimizer_len)
return min(candidate1, candidate2)
def kmer_to_uint(kmer):
''' Convers k-mer string to int '''
mapping = {
'A': 0,
'C': 1,
'G': 2,
'T': 3
}
res = 0
for symb in kmer:
res <<= 2
res += mapping[symb]
return res
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