1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
|
"""
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
class TestSplit(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_split.fastq')
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('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 check_one_read(self, read, length, start_seq, end_seq):
self.assertEqual(len(read[1]), length)
self.assertEqual(len(read[2]), length)
self.assertTrue(read[1].startswith(start_seq))
self.assertTrue(read[1].endswith(end_seq))
def test_split_1(self):
"""
When splitting is off, the reads aren't split.
"""
console_out = self.run_command('filtlong --min_length 1 -a ASSEMBLY INPUT > OUTPUT.fastq')
self.assertTrue('4 reads (11600 bp)' in console_out.replace(',', ''))
self.assertTrue('after splitting' not in console_out)
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 4)
def test_split_2(self):
"""
When the split threshold is over 200, no reads are split.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --split 250 INPUT > OUTPUT.fastq')
self.assertTrue('after splitting: 4 reads (11600 bp)' in console_out.replace(',', ''))
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 4)
for i in range(0, 4):
self.check_one_read(split_reads[i], 2900, b'TCATTACG', b'AAAAGGAC')
def test_split_3(self):
"""
When the split threshold is over 200, no reads are split.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --split 201 INPUT > OUTPUT.fastq')
self.assertTrue('after splitting: 4 reads (11600 bp)' in console_out.replace(',', ''))
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 4)
for i in range(0, 4):
self.check_one_read(split_reads[i], 2900, b'TCATTACG', b'AAAAGGAC')
def test_split_4(self):
"""
When the split threshold is exactly 200, only the last read is split.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --split 200 INPUT > OUTPUT.fastq')
self.assertTrue('after splitting: 5 reads (11400 bp)' in console_out.replace(',', ''))
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 5)
for i in range(0, 3):
self.check_one_read(split_reads[i], 2900, b'TCATTACG', b'AAAAGGAC')
self.check_one_read(split_reads[3], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[4], 1700, b'CCATGACA', b'AAAAGGAC')
def test_split_5(self):
"""
When the split threshold is between 150 and 200, only the last read is split.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --split 175 INPUT > OUTPUT.fastq')
self.assertTrue('after splitting: 5 reads (11400 bp)' in console_out.replace(',', ''))
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 5)
for i in range(0, 3):
self.check_one_read(split_reads[i], 2900, b'TCATTACG', b'AAAAGGAC')
self.check_one_read(split_reads[3], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[4], 1700, b'CCATGACA', b'AAAAGGAC')
def test_split_6(self):
"""
When the split threshold is between 50 and 100, tbe last two reads are split.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --split 75 INPUT > OUTPUT.fastq')
self.assertTrue('after splitting: 6 reads (11300 bp)' in console_out.replace(',', ''))
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 6)
for i in range(0, 2):
self.check_one_read(split_reads[i], 2900, b'TCATTACG', b'AAAAGGAC')
self.check_one_read(split_reads[2], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[3], 1800, b'GAAACGTG', b'AAAAGGAC')
self.check_one_read(split_reads[4], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[5], 1700, b'CCATGACA', b'AAAAGGAC')
def test_split_7(self):
"""
When the split threshold is between 50 and 100, tbe last two reads are split.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --split 51 INPUT > OUTPUT.fastq')
self.assertTrue('after splitting: 6 reads (11300 bp)' in console_out.replace(',', ''))
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 6)
for i in range(0, 2):
self.check_one_read(split_reads[i], 2900, b'TCATTACG', b'AAAAGGAC')
self.check_one_read(split_reads[2], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[3], 1800, b'GAAACGTG', b'AAAAGGAC')
self.check_one_read(split_reads[4], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[5], 1700, b'CCATGACA', b'AAAAGGAC')
def test_split_8(self):
"""
When the split threshold is exactly 50, tbe last three reads are split.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --split 50 INPUT > OUTPUT.fastq')
self.assertTrue('after splitting: 7 reads (11250 bp)' in console_out.replace(',', ''))
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 7)
self.check_one_read(split_reads[0], 2900, b'TCATTACG', b'AAAAGGAC')
self.check_one_read(split_reads[1], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[2], 1850, b'TGATGAAT', b'AAAAGGAC')
self.check_one_read(split_reads[3], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[4], 1800, b'GAAACGTG', b'AAAAGGAC')
self.check_one_read(split_reads[5], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[6], 1700, b'CCATGACA', b'AAAAGGAC')
def test_split_9(self):
"""
When the split threshold is less than 50, tbe last three reads are split.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --split 25 INPUT > OUTPUT.fastq')
self.assertTrue('after splitting: 7 reads (11250 bp)' in console_out.replace(',', ''))
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 7)
self.check_one_read(split_reads[0], 2900, b'TCATTACG', b'AAAAGGAC')
self.check_one_read(split_reads[1], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[2], 1850, b'TGATGAAT', b'AAAAGGAC')
self.check_one_read(split_reads[3], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[4], 1800, b'GAAACGTG', b'AAAAGGAC')
self.check_one_read(split_reads[5], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[6], 1700, b'CCATGACA', b'AAAAGGAC')
def test_split_10(self):
"""
Same as the previous test, but using reads as a reference.
"""
console_out = self.run_command('filtlong -1 ILLUMINA_1 -2 ILLUMINA_2 --split 25 INPUT > OUTPUT.fastq')
self.assertTrue('after splitting: 7 reads (11250 bp)' in console_out.replace(',', ''))
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 7)
self.check_one_read(split_reads[0], 2900, b'TCATTACG', b'AAAAGGAC')
self.check_one_read(split_reads[1], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[2], 1850, b'TGATGAAT', b'AAAAGGAC')
self.check_one_read(split_reads[3], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[4], 1800, b'GAAACGTG', b'AAAAGGAC')
self.check_one_read(split_reads[5], 1000, b'TCATTACG', b'ATTGGTTG')
self.check_one_read(split_reads[6], 1700, b'CCATGACA', b'AAAAGGAC')
def test_split_names(self):
"""
Makes sure the split reads are correctly named.
"""
console_out = self.run_command('filtlong -a ASSEMBLY --split 25 INPUT > OUTPUT.fastq')
split_reads = load_fastq(self.output_file)
self.assertEqual(len(split_reads), 7)
self.assertEqual(split_reads[0][0], b'test_split_1')
self.assertEqual(split_reads[1][0], b'test_split_2_1-1000')
self.assertEqual(split_reads[2][0], b'test_split_2_1051-2900')
self.assertEqual(split_reads[3][0], b'test_split_3_1-1000')
self.assertEqual(split_reads[4][0], b'test_split_3_1101-2900')
self.assertEqual(split_reads[5][0], b'test_split_4_1-1000')
self.assertEqual(split_reads[6][0], b'test_split_4_1201-2900')
|
