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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 shutil
import subprocess
import porechop.misc
class TestBarcodes(unittest.TestCase):
"""
Tests barcode demultiplexing.
"""
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_barcodes.fastq')
command = command.replace('porechop', runner_path)
command = command.replace('INPUT', input_path)
self.output_dir = 'TEMP_' + str(os.getpid())
command = command.replace('BARCODE_DIR', self.output_dir)
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.isdir(self.output_dir):
shutil.rmtree(self.output_dir)
def load_trimmed_reads(self, filename):
full_filepath = os.path.join(self.output_dir, filename)
trimmed_reads, read_type = porechop.misc.load_fasta_or_fastq(full_filepath)
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
def count_output_fastq_files(self):
return len([x for x in os.listdir(self.output_dir)
if os.path.isfile(os.path.join(self.output_dir, x)) and 'fastq' in x])
def test_barcodes_1(self):
"""
Tests with default settings.
"""
out, _ = self.run_command('porechop -i INPUT -b BARCODE_DIR')
self.assertEqual(self.count_output_fastq_files(), 4)
bc01_trimmed_reads = self.load_trimmed_reads('BC01.fastq')
bc02_trimmed_reads = self.load_trimmed_reads('BC02.fastq')
bc03_trimmed_reads = self.load_trimmed_reads('BC03.fastq')
none_trimmed_reads = self.load_trimmed_reads('none.fastq')
bc01_read_names = sorted(x[0] for x in bc01_trimmed_reads)
bc02_read_names = sorted(x[0] for x in bc02_trimmed_reads)
bc03_read_names = sorted(x[0] for x in bc03_trimmed_reads)
none_read_names = sorted(x[0] for x in none_trimmed_reads)
self.assertEqual(bc01_read_names, ['1', '4'])
self.assertEqual(bc02_read_names, ['2', '5'])
self.assertEqual(bc03_read_names, ['3'])
self.assertEqual(none_read_names, ['6', '8'])
self.assertEqual(sum(len(x[1]) for x in bc01_trimmed_reads), 8994)
self.assertEqual(sum(len(x[2]) for x in bc01_trimmed_reads), 8994)
self.assertTrue('BC01 2 8,994' in out)
self.assertEqual(sum(len(x[1]) for x in bc02_trimmed_reads), 9394)
self.assertEqual(sum(len(x[2]) for x in bc02_trimmed_reads), 9394)
self.assertTrue('BC02 2 9,394' in out)
self.assertEqual(sum(len(x[1]) for x in bc03_trimmed_reads), 6996)
self.assertEqual(sum(len(x[2]) for x in bc03_trimmed_reads), 6996)
self.assertTrue('BC03 1 6,996' in out)
self.assertEqual(sum(len(x[1]) for x in none_trimmed_reads), 13496)
self.assertEqual(sum(len(x[2]) for x in none_trimmed_reads), 13496)
self.assertTrue('none 2 13,496' in out)
self.assertTrue('Saving trimmed reads' in out)
def test_barcodes_2(self):
"""
Tests with --require_two_barcodes.
"""
out, _ = self.run_command('porechop -i INPUT -b BARCODE_DIR --require_two_barcodes')
self.assertEqual(self.count_output_fastq_files(), 4)
bc01_trimmed_reads = self.load_trimmed_reads('BC01.fastq')
bc02_trimmed_reads = self.load_trimmed_reads('BC02.fastq')
bc03_trimmed_reads = self.load_trimmed_reads('BC03.fastq')
none_trimmed_reads = self.load_trimmed_reads('none.fastq')
bc01_read_names = sorted(x[0] for x in bc01_trimmed_reads)
bc02_read_names = sorted(x[0] for x in bc02_trimmed_reads)
bc03_read_names = sorted(x[0] for x in bc03_trimmed_reads)
none_read_names = sorted(x[0] for x in none_trimmed_reads)
self.assertEqual(bc01_read_names, ['1'])
self.assertEqual(bc02_read_names, ['2'])
self.assertEqual(bc03_read_names, ['3'])
self.assertEqual(none_read_names, ['4', '5', '6', '8'])
self.assertEqual(sum(len(x[1]) for x in bc01_trimmed_reads), 4996)
self.assertEqual(sum(len(x[2]) for x in bc01_trimmed_reads), 4996)
self.assertTrue('BC01 1 4,996' in out)
self.assertEqual(sum(len(x[1]) for x in bc02_trimmed_reads), 6096)
self.assertEqual(sum(len(x[2]) for x in bc02_trimmed_reads), 6096)
self.assertTrue('BC02 1 6,096' in out)
self.assertEqual(sum(len(x[1]) for x in bc03_trimmed_reads), 6996)
self.assertEqual(sum(len(x[2]) for x in bc03_trimmed_reads), 6996)
self.assertTrue('BC03 1 6,996' in out)
self.assertEqual(sum(len(x[1]) for x in none_trimmed_reads), 20792)
self.assertEqual(sum(len(x[2]) for x in none_trimmed_reads), 20792)
self.assertTrue('none 4 20,792' in out)
self.assertTrue('Saving trimmed reads' in out)
def test_barcodes_3(self):
"""
Tests with --untrimmed.
"""
out, _ = self.run_command('porechop -i INPUT -b BARCODE_DIR --untrimmed')
self.assertEqual(self.count_output_fastq_files(), 4)
bc01_trimmed_reads = self.load_trimmed_reads('BC01.fastq')
bc02_trimmed_reads = self.load_trimmed_reads('BC02.fastq')
bc03_trimmed_reads = self.load_trimmed_reads('BC03.fastq')
none_trimmed_reads = self.load_trimmed_reads('none.fastq')
bc01_read_names = sorted(x[0] for x in bc01_trimmed_reads)
bc02_read_names = sorted(x[0] for x in bc02_trimmed_reads)
bc03_read_names = sorted(x[0] for x in bc03_trimmed_reads)
none_read_names = sorted(x[0] for x in none_trimmed_reads)
self.assertEqual(bc01_read_names, ['1', '4'])
self.assertEqual(bc02_read_names, ['2', '5'])
self.assertEqual(bc03_read_names, ['3'])
self.assertEqual(none_read_names, ['6', '8'])
self.assertEqual(sum(len(x[1]) for x in bc01_trimmed_reads), 9199)
self.assertEqual(sum(len(x[2]) for x in bc01_trimmed_reads), 9199)
self.assertTrue('BC01 2 9,199' in out)
self.assertEqual(sum(len(x[1]) for x in bc02_trimmed_reads), 9594)
self.assertEqual(sum(len(x[2]) for x in bc02_trimmed_reads), 9594)
self.assertTrue('BC02 2 9,594' in out)
self.assertEqual(sum(len(x[1]) for x in bc03_trimmed_reads), 7131)
self.assertEqual(sum(len(x[2]) for x in bc03_trimmed_reads), 7131)
self.assertTrue('BC03 1 7,131' in out)
self.assertEqual(sum(len(x[1]) for x in none_trimmed_reads), 13631)
self.assertEqual(sum(len(x[2]) for x in none_trimmed_reads), 13631)
self.assertTrue('none 2 13,631' in out)
self.assertTrue('Saving untrimmed reads' in out)
def test_barcodes_4(self):
"""
Tests with --discard_unassigned.
"""
out, _ = self.run_command('porechop -i INPUT -b BARCODE_DIR --discard_unassigned')
self.assertEqual(self.count_output_fastq_files(), 3)
bc01_trimmed_reads = self.load_trimmed_reads('BC01.fastq')
bc02_trimmed_reads = self.load_trimmed_reads('BC02.fastq')
bc03_trimmed_reads = self.load_trimmed_reads('BC03.fastq')
bc01_read_names = sorted(x[0] for x in bc01_trimmed_reads)
bc02_read_names = sorted(x[0] for x in bc02_trimmed_reads)
bc03_read_names = sorted(x[0] for x in bc03_trimmed_reads)
self.assertEqual(bc01_read_names, ['1', '4'])
self.assertEqual(bc02_read_names, ['2', '5'])
self.assertEqual(bc03_read_names, ['3'])
self.assertEqual(sum(len(x[1]) for x in bc01_trimmed_reads), 8994)
self.assertEqual(sum(len(x[2]) for x in bc01_trimmed_reads), 8994)
self.assertTrue('BC01 2 8,994' in out)
self.assertEqual(sum(len(x[1]) for x in bc02_trimmed_reads), 9394)
self.assertEqual(sum(len(x[2]) for x in bc02_trimmed_reads), 9394)
self.assertTrue('BC02 2 9,394' in out)
self.assertEqual(sum(len(x[1]) for x in bc03_trimmed_reads), 6996)
self.assertEqual(sum(len(x[2]) for x in bc03_trimmed_reads), 6996)
self.assertTrue('BC03 1 6,996' in out)
self.assertTrue('Saving trimmed reads' in out)
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