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"""
Copyright 2017 Ryan Wick (rrwick@gmail.com)
https://github.com/rrwick/Porechop
This module contains some tests for Porechop. To run them, execute `python3 -m unittest` from the
root Porechop directory.
This file is part of Porechop. Porechop is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by the Free Software Foundation,
either version 3 of the License, or (at your option) any later version. Porechop is distributed in
the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details. You should have received a copy of the GNU General Public License along with Porechop. If
not, see <http://www.gnu.org/licenses/>.
"""
import unittest
import os
import subprocess
import porechop.misc
class TestTwoAdapterSets(unittest.TestCase):
"""
This test set contains a combination of two adapter sets: SQK-MAP006 and SQK-NSK007
"""
def run_command(self, command):
runner_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'porechop-runner.py')
input_path = os.path.join(os.path.dirname(__file__), 'test_two_adapter_sets.fastq')
command = command.replace('porechop', runner_path)
command = command.replace('INPUT', input_path)
output_name = 'TEMP_' + str(os.getpid())
command = command.replace('OUTPUT', output_name)
try:
self.output_file = [x for x in command.split() if output_name in x][0]
except IndexError:
self.output_file = ''
p = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
out, err = p.communicate()
return out.decode(), err.decode()
def tearDown(self):
if os.path.isfile(self.output_file):
os.remove(self.output_file)
def load_trimmed_reads(self):
trimmed_reads, read_type = porechop.misc.load_fasta_or_fastq(self.output_file)
if read_type == 'FASTA':
trimmed_reads = [(x[2], x[1], '') for x in trimmed_reads]
else: # FASTQ
trimmed_reads = [(x[4], x[1], x[3]) for x in trimmed_reads]
return trimmed_reads, read_type
def check_trimmed_reads(self):
"""
This function checks all of the trimmed reads (assuming default settings).
"""
trimmed_reads, read_type = self.load_trimmed_reads()
# Read 1 isn't trimmed.
read_1 = trimmed_reads[0]
self.assertEqual(read_1[0], '1')
self.assertEqual(len(read_1[1]), 10000)
self.assertTrue(read_1[1].startswith('GCGGAAGTCA'))
self.assertTrue(read_1[1].endswith('TCCAGCCCCA'))
if read_type == 'FASTQ':
self.assertEqual(len(read_1[2]), 10000)
self.assertTrue(read_1[2].startswith("4,)4+311.'"))
self.assertTrue(read_1[2].endswith("3-16('...,"))
# Read 2 has an adapter trimmed from the start.
read_2 = trimmed_reads[1]
self.assertEqual(read_2[0], '2')
self.assertEqual(len(read_2[1]), 10970)
self.assertTrue(read_2[1].startswith('TGCAGCACAA'))
self.assertTrue(read_2[1].endswith('AAAGAACTGG'))
if read_type == 'FASTQ':
self.assertEqual(len(read_2[2]), 10970)
self.assertTrue(read_2[2].startswith("&)*-++$+,."))
self.assertTrue(read_2[2].endswith("(*'%)%.2+)"))
# Read 3 has an adapter trimmed from the start.
read_3 = trimmed_reads[2]
self.assertEqual(read_3[0], '3')
self.assertEqual(len(read_3[1]), 7970)
self.assertTrue(read_3[1].startswith('TATTTCGCTT'))
self.assertTrue(read_3[1].endswith('GAGAGTGTGA'))
if read_type == 'FASTQ':
self.assertEqual(len(read_3[2]), 7970)
self.assertTrue(read_3[2].startswith("2:2.4%%%)$"))
self.assertTrue(read_3[2].endswith("/-((+1-/%."))
# Read 4 has two internal adapters (from different sets).
read_4_1 = trimmed_reads[3]
read_4_2 = trimmed_reads[4]
read_4_3 = trimmed_reads[5]
self.assertEqual(read_4_1[0], '4_1')
self.assertEqual(read_4_2[0], '4_2')
self.assertEqual(read_4_3[0], '4_3')
self.assertEqual(len(read_4_1[1]), 1990)
self.assertEqual(len(read_4_2[1]), 2868)
self.assertEqual(len(read_4_3[1]), 1878)
self.assertTrue(read_4_1[1].startswith('TCATGACAGT'))
self.assertTrue(read_4_1[1].endswith('CGAAGTAGGG'))
self.assertTrue(read_4_2[1].startswith('ACGTGCTCGA'))
self.assertTrue(read_4_2[1].endswith('CCTTCCTAGA'))
self.assertTrue(read_4_3[1].startswith('GGCTCCCCCC'))
self.assertTrue(read_4_3[1].endswith('AGTTCTCGTG'))
if read_type == 'FASTQ':
self.assertEqual(len(read_4_1[2]), 1990)
self.assertEqual(len(read_4_2[2]), 2868)
self.assertEqual(len(read_4_3[2]), 1878)
self.assertTrue(read_4_1[2].startswith("45.2*25-',"))
self.assertTrue(read_4_1[2].endswith("$**+,,&$%3"))
self.assertTrue(read_4_2[2].startswith("]213438::5"))
self.assertTrue(read_4_2[2].endswith(".3/4:23]/]"))
self.assertTrue(read_4_3[2].startswith("0430/6202,"))
self.assertTrue(read_4_3[2].endswith("+2+,853322"))
return read_type
def test_results_normal_fastq(self):
self.run_command('porechop -i INPUT -o OUTPUT.fastq')
read_type = self.check_trimmed_reads()
self.assertEqual(read_type, 'FASTQ')
self.assertEqual(porechop.misc.get_compression_type(self.output_file), 'plain')
def test_results_gz_fastq(self):
self.run_command('porechop -i INPUT -o OUTPUT.fastq.gz')
read_type = self.check_trimmed_reads()
self.assertEqual(read_type, 'FASTQ')
self.assertEqual(porechop.misc.get_compression_type(self.output_file), 'gz')
def test_results_piped_fastq(self):
self.run_command('porechop -i INPUT > OUTPUT.fastq')
read_type = self.check_trimmed_reads()
self.assertEqual(read_type, 'FASTQ')
self.assertEqual(porechop.misc.get_compression_type(self.output_file), 'plain')
def test_check_reads_1(self):
"""
When only one read is checked, no adapters are found and nothing is trimmed.
"""
out, _ = self.run_command('porechop -i INPUT -o OUTPUT.fastq --check_reads 1')
self.assertTrue('No adapters found' in out)
trimmed_reads, read_type = self.load_trimmed_reads()
read_1 = [x for x in trimmed_reads if x[0] == '1'][0]
self.assertEqual(len(read_1[1]), 10000)
read_2 = [x for x in trimmed_reads if x[0] == '2'][0]
self.assertEqual(len(read_2[1]), 11000)
read_3 = [x for x in trimmed_reads if x[0] == '3'][0]
self.assertEqual(len(read_3[1]), 8000)
def test_check_reads_2(self):
"""
When only two reads are checked, only one adapter set is found.
"""
out, _ = self.run_command('porechop -i INPUT -o OUTPUT.fastq --check_reads 2')
self.assertTrue('Trimming adapters' in out)
self.assertTrue('SQK-MAP006_Y_Top_SK63:' in out)
self.assertTrue('SQK-MAP006_Y_Bottom_SK64:' in out)
trimmed_reads, read_type = self.load_trimmed_reads()
read_1 = [x for x in trimmed_reads if x[0] == '1'][0]
self.assertEqual(len(read_1[1]), 10000)
read_2 = [x for x in trimmed_reads if x[0] == '2'][0]
self.assertEqual(len(read_2[1]), 10970)
read_3 = [x for x in trimmed_reads if x[0] == '3'][0]
self.assertEqual(len(read_3[1]), 8000)
def test_check_reads_3(self):
"""
When three reads are checked, both adapter sets are found.
"""
out, _ = self.run_command('porechop -i INPUT -o OUTPUT.fastq --check_reads 3')
self.assertTrue('Trimming adapters' in out)
self.assertTrue('SQK-MAP006_Y_Top_SK63:' in out)
self.assertTrue('SQK-MAP006_Y_Bottom_SK64:' in out)
self.assertTrue('SQK-NSK007_Y_Top:' in out)
self.assertTrue('SQK-NSK007_Y_Bottom:' in out)
trimmed_reads, read_type = self.load_trimmed_reads()
read_1 = [x for x in trimmed_reads if x[0] == '1'][0]
self.assertEqual(len(read_1[1]), 10000)
read_2 = [x for x in trimmed_reads if x[0] == '2'][0]
self.assertEqual(len(read_2[1]), 10970)
read_3 = [x for x in trimmed_reads if x[0] == '3'][0]
self.assertEqual(len(read_3[1]), 7970)
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