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
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
|
"""
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 shutil
import porechop.misc
def get_read_type(filename):
_, read_type = porechop.misc.load_fasta_or_fastq(filename)
read_type = read_type.lower()
compression_type = porechop.misc.get_compression_type(filename)
if compression_type == 'plain':
return read_type
elif compression_type == 'gz':
return read_type + '.gz'
else:
assert False
class TestOutputFormat(unittest.TestCase):
def run_command(self, command, input_filename):
runner_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'porechop-runner.py')
input_path = os.path.join(os.path.dirname(__file__), input_filename)
command = command.replace('porechop', runner_path)
command = command.replace('IN', input_path)
output_name = 'TEMP_' + str(os.getpid())
command = command.replace('OUT', 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)
# The following tests use the auto format and should determine the output type using the output
# filename.
def test_auto_format_fastq_to_fastq(self):
self.run_command('porechop -i IN -o OUT.fastq', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fastq')
def test_auto_format_fastq_to_fastq_gz(self):
self.run_command('porechop -i IN -o OUT.fastq.gz', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fastq.gz')
def test_auto_format_fastq_to_fasta(self):
self.run_command('porechop -i IN -o OUT.fasta', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fasta')
def test_auto_format_fastq_to_fasta_gz(self):
self.run_command('porechop -i IN -o OUT.fasta.gz', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fasta.gz')
def test_auto_format_fastq_to_fastq_gz_weird_caps(self):
self.run_command('porechop -i IN -o OUT.fAsTq.Gz', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fastq.gz')
# The following tests use the auto format and pipe to output. They determine the output format
# from the input filename, but won't gzip the reads.
def test_auto_format_fastq_to_pipe(self):
self.run_command('porechop -i IN > OUT', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fastq')
def test_auto_format_fastq_gz_to_pipe(self):
self.run_command('porechop -i IN > OUT', 'test_format.fastq.gz')
self.assertEqual(get_read_type(self.output_file), 'fastq')
def test_auto_format_fasta_to_pipe(self):
self.run_command('porechop -i IN > OUT', 'test_format.fasta')
self.assertEqual(get_read_type(self.output_file), 'fasta')
def test_auto_format_fasta_gz_to_pipe(self):
self.run_command('porechop -i IN > OUT', 'test_format.fasta.gz')
self.assertEqual(get_read_type(self.output_file), 'fasta')
# The following tests explicitly set the output format.
def test_explicit_format_fastq_to_fastq(self):
self.run_command('porechop -i IN -o OUT --format fastq', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fastq')
def test_explicit_format_fastq_to_fastq_gz(self):
self.run_command('porechop -i IN -o OUT --format fastq.gz', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fastq.gz')
def test_explicit_format_fastq_to_fasta(self):
self.run_command('porechop -i IN -o OUT --format fasta', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fasta')
def test_explicit_format_fastq_to_fasta_gz(self):
self.run_command('porechop -i IN -o OUT --format fasta.gz', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fasta.gz')
def test_explicit_format_fasta_to_fasta(self):
self.run_command('porechop -i IN -o OUT --format fasta', 'test_format.fasta')
self.assertEqual(get_read_type(self.output_file), 'fasta')
def test_explicit_format_fasta_to_fasta_gz(self):
self.run_command('porechop -i IN -o OUT --format fasta.gz', 'test_format.fasta')
self.assertEqual(get_read_type(self.output_file), 'fasta.gz')
# For these tests the output filename conflicts with the requested format. The requested format
# should be followed, not the filename.
def test_explicit_format_fastq_to_fastq_conflicting_name_1(self):
self.run_command('porechop -i IN -o OUT.fasta --format fastq', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fastq')
def test_explicit_format_fastq_to_fastq_conflicting_name_2(self):
self.run_command('porechop -i IN -o OUT.fasta.gz --format fastq', 'test_format.fastq.gz')
self.assertEqual(get_read_type(self.output_file), 'fastq')
def test_explicit_format_fastq_to_fasta_gz_conflicting_name_1(self):
self.run_command('porechop -i IN -o OUT.fastq --format fasta.gz', 'test_format.fastq')
self.assertEqual(get_read_type(self.output_file), 'fasta.gz')
def test_explicit_format_fastq_to_fasta_gz_conflicting_name_2(self):
self.run_command('porechop -i IN -o OUT.fastq.gz --format fasta.gz', 'test_format.fasta')
self.assertEqual(get_read_type(self.output_file), 'fasta.gz')
class TestOutputFormatBarcodes(unittest.TestCase):
def run_command(self, command, input_filename):
runner_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'porechop-runner.py')
input_path = os.path.join(os.path.dirname(__file__), input_filename)
command = command.replace('porechop', runner_path)
command = command.replace('IN', input_path)
self.output_dir = 'TEMP_' + str(os.getpid())
command = command.replace('B_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 check_output_file_formats(self, output_files, expected_format):
for output_file in [os.path.join(self.output_dir, x) for x in output_files]:
self.assertTrue(os.path.isfile(output_file))
self.assertEqual(get_read_type(output_file), expected_format)
# The following tests use the auto format and should determine the output type using the input
# type.
def test_auto_format_fastq_to_fastq(self):
self.run_command('porechop -i IN -b B_DIR', 'test_format_barcodes.fastq')
self.check_output_file_formats(['BC01.fastq', 'BC02.fastq', 'BC03.fastq', 'none.fastq'],
'fastq')
def test_auto_format_fastq_gz_to_fastq_gz(self):
self.run_command('porechop -i IN -b B_DIR', 'test_format_barcodes.fastq.gz')
self.check_output_file_formats(['BC01.fastq.gz', 'BC02.fastq.gz', 'BC03.fastq.gz',
'none.fastq.gz'], 'fastq.gz')
def test_auto_format_fasta_to_fasta(self):
self.run_command('porechop -i IN -b B_DIR', 'test_format_barcodes.fasta')
self.check_output_file_formats(['BC01.fasta', 'BC02.fasta', 'BC03.fasta', 'none.fasta'],
'fasta')
def test_auto_format_fasta_gz_to_fasta_gz(self):
self.run_command('porechop -i IN -b B_DIR', 'test_format_barcodes.fasta.gz')
self.check_output_file_formats(['BC01.fasta.gz', 'BC02.fasta.gz', 'BC03.fasta.gz',
'none.fasta.gz'], 'fasta.gz')
# The following tests explicitly set the output format.
def test_explicit_format_fastq_to_fastq(self):
self.run_command('porechop -i IN -b B_DIR --format fastq', 'test_format_barcodes.fastq')
self.check_output_file_formats(['BC01.fastq', 'BC02.fastq', 'BC03.fastq', 'none.fastq'],
'fastq')
def test_explicit_format_fastq_to_fastq_gz(self):
self.run_command('porechop -i IN -b B_DIR --format fastq.gz', 'test_format_barcodes.fastq')
self.check_output_file_formats(['BC01.fastq.gz', 'BC02.fastq.gz', 'BC03.fastq.gz',
'none.fastq.gz'], 'fastq.gz')
def test_explicit_format_fastq_gz_to_fastq(self):
self.run_command('porechop -i IN -b B_DIR --format fastq', 'test_format_barcodes.fastq.gz')
self.check_output_file_formats(['BC01.fastq', 'BC02.fastq', 'BC03.fastq', 'none.fastq'],
'fastq')
def test_explicit_format_fastq_gz_to_fastq_gz(self):
self.run_command('porechop -i IN -b B_DIR --format fastq.gz',
'test_format_barcodes.fastq.gz')
self.check_output_file_formats(['BC01.fastq.gz', 'BC02.fastq.gz', 'BC03.fastq.gz',
'none.fastq.gz'], 'fastq.gz')
def test_explicit_format_fastq_to_fasta(self):
self.run_command('porechop -i IN -b B_DIR --format fasta', 'test_format_barcodes.fastq')
self.check_output_file_formats(['BC01.fasta', 'BC02.fasta', 'BC03.fasta', 'none.fasta'],
'fasta')
def test_explicit_format_fastq_to_fasta_gz(self):
self.run_command('porechop -i IN -b B_DIR --format fasta.gz', 'test_format_barcodes.fastq')
self.check_output_file_formats(['BC01.fasta.gz', 'BC02.fasta.gz', 'BC03.fasta.gz',
'none.fasta.gz'], 'fasta.gz')
def test_explicit_format_fasta_to_fasta(self):
self.run_command('porechop -i IN -b B_DIR --format fasta', 'test_format_barcodes.fasta')
self.check_output_file_formats(['BC01.fasta', 'BC02.fasta', 'BC03.fasta', 'none.fasta'],
'fasta')
def test_explicit_format_fasta_to_fasta_gz(self):
self.run_command('porechop -i IN -b B_DIR --format fasta.gz', 'test_format_barcodes.fasta')
self.check_output_file_formats(['BC01.fasta.gz', 'BC02.fasta.gz', 'BC03.fasta.gz',
'none.fasta.gz'], 'fasta.gz')
def test_explicit_format_fasta_gz_to_fasta(self):
self.run_command('porechop -i IN -b B_DIR --format fasta', 'test_format_barcodes.fasta.gz')
self.check_output_file_formats(['BC01.fasta', 'BC02.fasta', 'BC03.fasta', 'none.fasta'],
'fasta')
def test_explicit_format_fasta_gz_to_fasta_gz(self):
self.run_command('porechop -i IN -b B_DIR --format fasta.gz',
'test_format_barcodes.fasta.gz')
self.check_output_file_formats(['BC01.fasta.gz', 'BC02.fasta.gz', 'BC03.fasta.gz',
'none.fasta.gz'], 'fasta.gz')
|
