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"""
Copyright 2017 Ryan Wick (rrwick@gmail.com)
https://github.com/rrwick/Filtlong
This module contains some tests for Filtlong. To run them, execute `python3 -m unittest` from the
root Filtlong directory.
This file is part of Filtlong. Filtlong 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. Filtlong 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 Filtlong. If
not, see <http://www.gnu.org/licenses/>.
"""
import unittest
import os
import subprocess
def load_fastq(filename):
reads = []
with open(filename, 'rb') as fastq:
for line in fastq:
stripped_line = line.strip()
if len(stripped_line) == 0:
continue
if not stripped_line.startswith(b'@'):
continue
name = stripped_line[1:].split()[0]
sequence = next(fastq).strip()
_ = next(fastq)
qualities = next(fastq).strip()
reads.append((name, sequence, qualities))
return reads
def load_fasta(filename):
reads = []
with open(filename, 'rb') as fastq:
for line in fastq:
stripped_line = line.strip()
if len(stripped_line) == 0:
continue
if not stripped_line.startswith(b'>'):
continue
name = stripped_line[1:].split()[0]
sequence = next(fastq).strip()
reads.append((name, sequence))
return reads
class TestSort(unittest.TestCase):
def run_command(self, command):
binary_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'bin', 'filtlong')
input_path = os.path.join(os.path.dirname(__file__), 'test_sort.fastq')
input_fasta = os.path.join(os.path.dirname(__file__), 'test_sort.fasta')
assembly_reference = os.path.join(os.path.dirname(__file__), 'test_reference.fasta')
illumina_reference_1 = os.path.join(os.path.dirname(__file__), 'test_reference_1.fastq.gz')
illumina_reference_2 = os.path.join(os.path.dirname(__file__), 'test_reference_2.fastq.gz')
command = command.replace('filtlong', binary_path)
command = command.replace('INPUT', input_path)
command = command.replace('FASTA', input_fasta)
command = command.replace('ASSEMBLY', assembly_reference)
command = command.replace('ILLUMINA_1', illumina_reference_1)
command = command.replace('ILLUMINA_2', illumina_reference_2)
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)
_, err = p.communicate()
return err.decode()
def tearDown(self):
if os.path.isfile(self.output_file):
os.remove(self.output_file)
def test_sort_high_threshold_1(self):
"""
With a high input threshold, all three reads should be outputted.
"""
console_out = self.run_command('filtlong --target_bases 100000 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))
self.assertTrue('not enough reads to reach target' in console_out)
def test_sort_high_threshold_1_assembly_ref(self):
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 100000 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))
self.assertTrue('not enough reads to reach target' in console_out)
def test_sort_high_threshold_1_read_ref(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 100000 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))
self.assertTrue('not enough reads to reach target' in console_out)
def test_sort_high_threshold_1_assembly_ref_fasta(self):
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 100000 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))
self.assertTrue('not enough reads to reach target' in console_out)
def test_sort_high_threshold_1_read_ref_fasta(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 100000 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
self.assertTrue('target: 100000 bp' in console_out.replace(',', ''))
self.assertTrue('not enough reads to reach target' in console_out)
def test_sort_high_threshold_2(self):
"""
With an input threshold of just over 10000, all three reads should be outputted.
"""
console_out = self.run_command('filtlong --target_bases 10001 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
self.assertTrue('target: 10001 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 15000 bp' in console_out.replace(',', ''))
def test_sort_high_threshold_2_assembly_ref(self):
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 10001 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
self.assertTrue('target: 10001 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 15000 bp' in console_out.replace(',', ''))
def test_sort_high_threshold_2_read_ref(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 10001 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
self.assertTrue('target: 10001 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 15000 bp' in console_out.replace(',', ''))
def test_sort_high_threshold_2_assembly_ref_fasta(self):
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 10001 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
self.assertTrue('target: 10001 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 15000 bp' in console_out.replace(',', ''))
def test_sort_high_threshold_2_read_ref_fasta(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 10001 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_2', 'test_sort_3'])
self.assertTrue('target: 10001 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 15000 bp' in console_out.replace(',', ''))
def test_sort_medium_threshold_1(self):
"""
With an input threshold of exactly 10000, only two reads should be outputted. Read 1 is the worst (by Phred
score), so just reads 2 and 3.
"""
console_out = self.run_command('filtlong --target_bases 10000 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_2', 'test_sort_3'])
self.assertTrue('target: 10000 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
def test_sort_medium_threshold_1_assembly_ref(self):
"""
With a reference, reads 1 and 3 are the best two (instead of reads 2 and 3).
"""
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 10000 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
self.assertTrue('target: 10000 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
def test_sort_medium_threshold_1_read_ref(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 10000 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
self.assertTrue('target: 10000 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
def test_sort_medium_threshold_1_assembly_ref_fasta(self):
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 10000 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
self.assertTrue('target: 10000 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
def test_sort_medium_threshold_1_read_ref_fasta(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 10000 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
self.assertTrue('target: 10000 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
def test_sort_medium_threshold_2(self):
"""
With an input threshold of just over 5000, two reads should be outputted.
"""
console_out = self.run_command('filtlong --target_bases 5001 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_2', 'test_sort_3'])
self.assertTrue('target: 5001 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
def test_sort_medium_threshold_2_assembly_ref(self):
"""
With a reference, reads 1 and 3 are the best two (instead of reads 2 and 3).
"""
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 5001 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
self.assertTrue('target: 5001 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
def test_sort_medium_threshold_2_read_ref(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 5001 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
self.assertTrue('target: 5001 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
def test_sort_medium_threshold_2_assembly_ref_fasta(self):
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 5001 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
self.assertTrue('target: 5001 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
def test_sort_medium_threshold_2_read_ref_fasta(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 5001 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1', 'test_sort_3'])
self.assertTrue('target: 5001 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 10000 bp' in console_out.replace(',', ''))
def test_sort_low_threshold_1(self):
"""
With an input threshold of exactly 5000, only one read should be outputted: read 2 (best by Phred score).
"""
console_out = self.run_command('filtlong --target_bases 5000 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_2'])
self.assertTrue('target: 5000 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
def test_sort_low_threshold_1_assembly_ref(self):
"""
With a reference (instead of Phred), read 1 is the best.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 5000 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1'])
self.assertTrue('target: 5000 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
def test_sort_low_threshold_1_read_ref(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 5000 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1'])
self.assertTrue('target: 5000 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
def test_sort_low_threshold_1_assembly_ref_fasta(self):
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 5000 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1'])
self.assertTrue('target: 5000 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
def test_sort_low_threshold_1_read_ref_fasta(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 5000 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1'])
self.assertTrue('target: 5000 bp' in console_out.replace(',', ''))
self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
def test_sort_low_threshold_2(self):
"""
With an input threshold of 1, only one read should be outputted: read 2 (best by Phred score).
"""
console_out = self.run_command('filtlong --target_bases 1 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_2'])
self.assertTrue('target: 1 bp' in console_out)
self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
def test_sort_low_threshold_2_assembly_ref(self):
"""
With a reference (instead of Phred), read 1 is the best.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 1 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1'])
self.assertTrue('target: 1 bp' in console_out)
self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
def test_sort_low_threshold_2_read_ref(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 1 INPUT > OUTPUT.fastq')
output_reads = load_fastq(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1'])
self.assertTrue('target: 1 bp' in console_out)
self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
def test_sort_low_threshold_2_assembly_ref_fasta(self):
console_out = self.run_command('filtlong -a ASSEMBLY --target_bases 1 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1'])
self.assertTrue('target: 1 bp' in console_out)
self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
def test_sort_low_threshold_2_read_ref_fasta(self):
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --target_bases 1 FASTA > OUTPUT.fastq')
output_reads = load_fasta(self.output_file)
read_names = [x[0].decode() for x in output_reads]
self.assertEqual(read_names, ['test_sort_1'])
self.assertTrue('target: 1 bp' in console_out)
self.assertTrue('keeping 5000 bp' in console_out.replace(',', ''))
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