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test_kmerDecoder.py
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test_kmerDecoder.py
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import os
import shutil
import unittest
import random
import kProcessor as kp
from params import test_params
import pytest
class TestkmerDecoder(unittest.TestCase):
generic_params = test_params(10, "PHMAP")
seq = "ACGTAGCATGCATGACGATGCTAGCGTGATGCTAGCTAGTCAGTAGCATGC"
def test_kmers(self):
KD_params = {
"mode": "kmers",
"params": {
"k_size": 10,
}
}
KD_seq = kp.initialize_kmerDecoder(KD_params["mode"], KD_params["params"])
KF_seq = kp.kDataFramePHMAP(KD_params["params"]["k_size"])
KD_file = kp.initialize_kmerDecoder(self.generic_params.small_fasta_file, 1, KD_params["mode"], KD_params["params"])
KF_file = kp.kDataFramePHMAP(KD_params["params"]["k_size"])
kp.parseSequences(KD_file, KF_file)
self.assertFalse(KF_file.empty())
kp.parseSequencesFromString(KD_seq, self.seq, KF_seq)
self.assertFalse(KF_seq.empty())
self.assertEqual(KF_seq.size(), KF_file.size())
def test_skipmers(self):
KD_params = {
"mode": "skipmers",
"params": {
"k_size": 10,
"m": 2,
"n": 3
}
}
KD_seq = kp.initialize_kmerDecoder(KD_params["mode"], KD_params["params"])
KF_seq = kp.kDataFramePHMAP(KD_params["params"]["k_size"])
KD_file = kp.initialize_kmerDecoder(self.generic_params.small_fasta_file, 1, KD_params["mode"], KD_params["params"])
KF_file = kp.kDataFramePHMAP(KD_params["params"]["k_size"])
kp.parseSequences(KD_file, KF_file)
self.assertFalse(KF_file.empty())
kp.parseSequencesFromString(KD_seq, self.seq, KF_seq)
self.assertFalse(KF_seq.empty())
self.assertEqual(KF_seq.size(), KF_file.size())
def test_minimizers(self):
KD_params = {
"mode": "minimizers",
"params": {
"k_size": 5,
"w": 10,
}
}
KD_seq = kp.initialize_kmerDecoder(KD_params["mode"], KD_params["params"])
KF_seq = kp.kDataFramePHMAP(KD_params["params"]["k_size"])
KD_file = kp.initialize_kmerDecoder(self.generic_params.small_fasta_file, 1, KD_params["mode"], KD_params["params"])
KF_file = kp.kDataFramePHMAP(KD_params["params"]["k_size"])
kp.parseSequences(KD_file, KF_file)
self.assertFalse(KF_file.empty())
kp.parseSequencesFromString(KD_seq, self.seq, KF_seq)
self.assertFalse(KF_seq.empty())
self.assertEqual(KF_seq.size(), KF_file.size())