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test_kmerCounting.py
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test_kmerCounting.py
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import os
import shutil
import unittest
import random
import kProcessor as kp
from params import test_params
class TestkmerCounting(unittest.TestCase):
ksize = 21
def test_kmerCountingFASTQ(self):
params_MQF = test_params(self.ksize, "MQF")
params_PHMAP = test_params(self.ksize, "PHMAP")
params_MAP = test_params(self.ksize, "MAP")
KD_MQF = kp.initialize_kmerDecoder(params_MQF.fastqFiles[0], 1000, "kmers", {"k_size": self.ksize})
KD_PHMAP = kp.initialize_kmerDecoder(params_PHMAP.fastqFiles[0], 1000, "kmers", {"k_size": self.ksize})
KD_MAP = kp.initialize_kmerDecoder(params_MAP.fastqFiles[0], 1000, "kmers", {"k_size": self.ksize})
KF_MQF = params_MQF.new_kf(self.ksize)
KF_PHMAP = params_PHMAP.new_kf(self.ksize)
KF_MAP = params_MAP.new_kf(self.ksize)
# kmerCounting
kp.parseSequences(KD_MQF, KF_MQF)
kp.parseSequences(KD_PHMAP, KF_PHMAP)
kp.parseSequences(KD_MAP, KF_MAP)
self.assertTrue(KF_MQF.size())
self.assertTrue(KF_PHMAP.size())
self.assertTrue(KF_MAP.size())
def test_kmerCountingFASTA(self):
params_MQF = test_params(self.ksize, "MQF")
params_PHMAP = test_params(self.ksize, "PHMAP")
params_MAP = test_params(self.ksize, "MAP")
KD_MQF = kp.initialize_kmerDecoder(params_MQF.fasta_file, 1000, "kmers", {"k_size": self.ksize})
KD_PHMAP = kp.initialize_kmerDecoder(params_PHMAP.fasta_file, 1000, "kmers", {"k_size": self.ksize})
KD_MAP = kp.initialize_kmerDecoder(params_MAP.fasta_file, 1000, "kmers", {"k_size": self.ksize})
KF_MQF = params_MQF.new_kf(self.ksize)
KF_PHMAP = params_PHMAP.new_kf(self.ksize)
KF_MAP = params_MAP.new_kf(self.ksize)
self.assertFalse(KF_MQF.size())
self.assertFalse(KF_PHMAP.size())
self.assertFalse(KF_MAP.size())
# kmerCounting
kp.parseSequences(KD_MQF, KF_MQF)
kp.parseSequences(KD_PHMAP, KF_PHMAP)
kp.parseSequences(KD_MAP, KF_MAP)
self.assertTrue(KF_MQF.size())
self.assertTrue(KF_PHMAP.size())
self.assertTrue(KF_MAP.size())