forked from biopython/biopython
/
test_samtools_tool.py
276 lines (244 loc) · 10.5 KB
/
test_samtools_tool.py
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
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
# Copyright 2014 by Saket Choudhary. Based on test_Clustalw_tool.py by Peter
# Cock .
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# Last Checked with samtools [0.1.18 (r982:295)]
"""Tests for samtools tool."""
from Bio import MissingExternalDependencyError
import sys
import os
import unittest
from Bio.Application import ApplicationError
from Bio.Sequencing.Applications import SamtoolsViewCommandline
from Bio.Sequencing.Applications import SamtoolsCalmdCommandline
from Bio.Sequencing.Applications import SamtoolsCatCommandline
from Bio.Sequencing.Applications import SamtoolsFaidxCommandline
from Bio.Sequencing.Applications import SamtoolsIdxstatsCommandline
from Bio.Sequencing.Applications import SamtoolsIndexCommandline
from Bio.Sequencing.Applications import SamtoolsMergeCommandline
from Bio.Sequencing.Applications import SamtoolsMpileupCommandline
from Bio.Sequencing.Applications import SamtoolsVersion1xSortCommandline
from Bio.Sequencing.Applications import SamtoolsSortCommandline
# TODO from Bio.Sequencing.Applications import SamtoolsPhaseCommandline
# TODO from Bio.Sequencing.Applications import SamtoolsReheaderCommandline
# TODO from Bio.Sequencing.Applications import SamtoolsRmdupCommandline
# TODO from Bio.Sequencing.Applications import SamtoolsTargetcutCommandline
# TODO from Bio.Sequencing.Applications import SamtoolsFixmateCommandline
#################################################################
SamtoolsVersion0xSortCommandline = SamtoolsSortCommandline
# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"
samtools_exe = None
if sys.platform == "win32":
# TODO - Check the path?
try:
# This can vary depending on the Windows language.
prog_files = os.environ["PROGRAMFILES"]
except KeyError:
prog_files = r"C:\Program Files"
# By default tries C:\Program Files\samtools\samtools.exe
# or C:\Program Files\samtools.exe was chosen
likely_dirs = ["samtools", ""]
likely_exes = ["samtools.exe"]
for folder in likely_dirs:
if os.path.isdir(os.path.join(prog_files, folder)):
for filename in likely_exes:
if os.path.isfile(os.path.join(prog_files, folder, filename)):
samtools_exe = os.path.join(prog_files, folder, filename)
break
if samtools_exe:
break
else:
from subprocess import getoutput
output = getoutput("samtools")
# Since "not found" may be in another language, try and be sure this is
# really the samtools tool's output
if (
"not found" not in output
and "samtools (Tools for alignments in the SAM format)" in output
):
samtools_exe = "samtools"
if not samtools_exe:
raise MissingExternalDependencyError(
"""Install samtools and correctly set the file path to the program
if you want to use it from Biopython"""
)
class SamtoolsTestCase(unittest.TestCase):
"""Class for implementing Samtools test cases."""
def setUp(self):
self.files_to_clean = set()
self.samfile1 = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "SamBam", "sam1.sam"
)
self.reference = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"BWA",
"human_g1k_v37_truncated.fasta",
)
self.referenceindexfile = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"BWA",
"human_g1k_v37_truncated.fasta.fai",
)
self.samfile2 = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "SamBam", "sam2.sam"
)
self.bamfile1 = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "SamBam", "bam1.bam"
)
self.bamfile2 = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "SamBam", "bam2.bam"
)
self.outsamfile = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "SamBam", "out.sam"
)
self.outbamfile = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "SamBam", "out.bam"
)
self.bamindexfile1 = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "SamBam", "bam1.bam.bai"
)
self.sortedbamfile1 = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "SamBam", "bam1_sorted.bam"
)
self.sortedbamfile2 = os.path.join(
os.path.dirname(os.path.abspath(__file__)), "SamBam", "bam2_sorted.bam"
)
self.files_to_clean = [
self.referenceindexfile,
self.bamindexfile1,
self.outbamfile,
]
def tearDown(self):
for filename in self.files_to_clean:
if os.path.isfile(filename):
os.remove(filename)
def test_view(self):
"""Test for samtools view."""
cmdline = SamtoolsViewCommandline(samtools_exe)
cmdline.set_parameter("input_file", self.bamfile1)
stdout_bam, stderr_bam = cmdline()
self.assertTrue(
stderr_bam.startswith(""),
"SAM file viewing failed: \n%s\nStdout:%s" % (cmdline, stdout_bam),
)
cmdline.set_parameter("input_file", self.samfile1)
cmdline.set_parameter("S", True)
stdout_sam, stderr_sam = cmdline()
self.assertTrue(
stdout_sam.startswith("HWI-1KL120:88:D0LRBACXX:1:1101:1780:2146"),
"SAM file viewing failed:\n%s\nStderr:%s" % (cmdline, stderr_sam),
)
def create_fasta_index(self):
"""Create index for reference fasta sequence."""
cmdline = SamtoolsFaidxCommandline(samtools_exe)
cmdline.set_parameter("reference", self.reference)
stdout, stderr = cmdline()
def create_bam_index(self, input_bam):
"""Create index of an input bam file."""
cmdline = SamtoolsIndexCommandline(samtools_exe)
cmdline.set_parameter("input_bam", input_bam)
stdout, stderr = cmdline()
def test_faidx(self):
cmdline = SamtoolsFaidxCommandline(samtools_exe)
cmdline.set_parameter("reference", self.reference)
stdout, stderr = cmdline()
self.assertFalse(
stderr, "Samtools faidx failed:\n%s\nStderr:%s" % (cmdline, stderr)
)
self.assertTrue(os.path.isfile(self.referenceindexfile))
def test_calmd(self):
"""Test for samtools calmd."""
self.create_fasta_index()
cmdline = SamtoolsCalmdCommandline(samtools_exe)
cmdline.set_parameter("reference", self.reference)
cmdline.set_parameter("input_bam", self.bamfile1)
# If there is no index file for the reference
# samtools calmd creates one at the time of calling
if os.path.exists(self.referenceindexfile):
# print("exists")
stderr_calmd_expected = ""
else:
# print("doesnt exist")
stderr_calmd_expected = "[fai_load] build FASTA index.\n"
stdout, stderr = cmdline()
self.assertEqual(stderr, stderr_calmd_expected)
def test_cat(self):
cmdline = SamtoolsCatCommandline(samtools_exe)
cmdline.set_parameter("o", self.outbamfile)
cmdline.set_parameter("input_bam", [self.bamfile1, self.bamfile2])
stdout, stderr = cmdline()
self.assertEqual(stderr, "")
# TODO: def test_fixmate(self):
def test_sort(self):
cmdline = SamtoolsVersion0xSortCommandline(samtools_exe)
cmdline.set_parameter("input", self.bamfile1)
cmdline.set_parameter("out_prefix", "SamBam/out")
try:
stdout, stderr = cmdline()
except ApplicationError as err:
if (
"[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files"
in str(err)
):
cmdline = SamtoolsVersion1xSortCommandline(samtools_exe)
cmdline.set_parameter("input", self.bamfile1)
cmdline.set_parameter("-T", "out")
cmdline.set_parameter("-o", "out.bam")
try:
stdout, stderr = cmdline()
except ApplicationError:
raise
else:
raise
self.assertFalse(
stderr, "Samtools sort failed:\n%s\nStderr:%s" % (cmdline, stderr)
)
def test_index(self):
cmdline = SamtoolsIndexCommandline(samtools_exe)
cmdline.set_parameter("input_bam", self.bamfile1)
stdout, stderr = cmdline()
self.assertFalse(
stderr, "Samtools index failed:\n%s\nStderr:%s" % (cmdline, stderr)
)
self.assertTrue(os.path.exists(self.bamindexfile1))
def test_idxstats(self):
self.create_bam_index(self.bamfile1)
cmdline = SamtoolsIdxstatsCommandline(samtools_exe)
cmdline.set_parameter("input_bam", self.bamfile1)
stdout, stderr = cmdline()
self.assertFalse(
stderr, "Samtools idxstats failed:\n%s\nStderr:%s" % (cmdline, stderr)
)
def test_merge(self):
cmdline = SamtoolsMergeCommandline(samtools_exe)
cmdline.set_parameter("input_bam", [self.bamfile1, self.bamfile2])
cmdline.set_parameter("out_bam", self.outbamfile)
cmdline.set_parameter("f", True) # Overwrite out.bam if it exists
stdout, stderr = cmdline()
# Worked up to v1.2, then there was a regression failing with message
# but as of v1.3 expect a warning: [W::bam_merge_core2] No @HD tag found.
self.assertTrue(
not stderr or stderr.strip() == "[W::bam_merge_core2] No @HD tag found.",
"Samtools merge failed:\n%s\nStderr:%s" % (cmdline, stderr),
)
self.assertTrue(os.path.exists(self.outbamfile))
def test_mpileup(self):
cmdline = SamtoolsMpileupCommandline(samtools_exe)
cmdline.set_parameter("input_file", [self.bamfile1])
stdout, stderr = cmdline()
self.assertNotIn("[bam_pileup_core]", stdout)
def test_mpileup_list(self):
cmdline = SamtoolsMpileupCommandline(samtools_exe)
cmdline.set_parameter("input_file", [self.sortedbamfile1, self.sortedbamfile2])
stdout, stderr = cmdline()
self.assertNotIn("[bam_pileup_core]", stdout)
# TODO: def test_phase(self):
# TODO: def test_reheader(self):
# TODO: def test_rmdup(self):
# TODO: def test_targetcut(self):
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)