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from .cgr import CGR
from itertools import product
from collections import defaultdict
import numpy as np
class FCGR(CGR):
"""Frequency matrix CGR
an (2**k x 2**k) 2D representation will be created for a
n-long sequence.
- k represents the k-mer.
- 2**k x 2**k = 4**k the total number of k-mers (sequences of length k)
- pixel value correspond to the value of the frequency for each k-mer
"""
def __init__(self, k: int,):
super().__init__()
self.k = k # k-mer representation
self.kmers = list("".join(kmer) for kmer in product("ACGT", repeat=self.k))
self.kmer2pixel = self.kmer2pixel_position()
def __call__(self, sequence: str):
"Given a DNA sequence, returns an array with his frequencies in the same order as FCGR"
self.count_kmers(sequence)
# Create an empty array to save the FCGR values
array_size = int(2**self.k)
freq_matrix = np.zeros((array_size,array_size))
# Assign frequency to each box in the matrix
for kmer, freq in self.freq_kmer.items():
pos_x, pos_y = self.kmer2pixel[kmer]
freq_matrix[int(pos_x)-1,int(pos_y)-1] = freq
return freq_matrix
def count_kmer(self, kmer):
if "N" not in kmer:
self.freq_kmer[kmer] += 1
def count_kmers(self, sequence: str):
self.freq_kmer = defaultdict(int)
# representativity of kmers
last_j = len(sequence) - self.k + 1
kmers = (sequence[i:(i+self.k)] for i in range(last_j))
# count kmers in a dictionary
list(self.count_kmer(kmer) for kmer in kmers)
def kmer_probabilities(self, sequence: str):
self.probabilities = defaultdict(float)
N=len(sequence)
for key, value in self.freq_kmer.items():
self.probabilities[key] = float(value) / (N - self.k + 1)
def pixel_position(self, kmer: str):
"Get pixel position in the FCGR matrix for a k-mer"
coords = self.encode(kmer)
N,x,y = coords.N, coords.x, coords.y
# Coordinates from [-1,1]² to [1,2**k]²
np_coords = np.array([(x + 1)/2, (y + 1)/2]) # move coordinates from [-1,1]² to [0,1]²
np_coords *= 2**self.k # rescale coordinates from [0,1]² to [0,2**k]²
x,y = np.ceil(np_coords) # round to upper integer
# Turn coordinates (cx,cy) into pixel (px,py) position
# px = 2**k-cy+1, py = cx
return 2**self.k-int(y)+1, int(x)
def kmer2pixel_position(self,):
kmer2pixel = dict()
for kmer in self.kmers:
kmer2pixel[kmer] = self.pixel_position(kmer)
return kmer2pixel |