File: samtools_test.py

package info (click to toggle)
python-pysam 0.15.4+ds-3
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, sid
  • size: 27,992 kB
  • sloc: ansic: 140,738; python: 7,881; sh: 265; makefile: 223; perl: 41
file content (423 lines) | stat: -rw-r--r-- 14,939 bytes parent folder | download
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
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
#!/usr/bin/env python
'''unit testing code for pysam.

Execute in the :file:`tests` directory as it requires the Makefile
and data files located there.
'''

import warnings
import unittest
import os
import re
import glob
import sys
import subprocess
import shutil
import pysam
import pysam.samtools
import pysam.bcftools
from TestUtils import checkBinaryEqual, check_lines_equal, \
    check_samtools_view_equal, get_temp_filename, force_bytes, WORKDIR, \
    BAM_DATADIR


IS_PYTHON3 = sys.version_info[0] >= 3


def run_command(cmd):
    '''run a samtools command'''
    try:
        retcode = subprocess.call(cmd, shell=True,
                                  stderr=subprocess.PIPE)
        if retcode < 0:
            print("Child was terminated by signal", -retcode)
    except OSError as e:
        print("Execution failed:", e)


def get_version(executable):
    '''return samtools/bcftools version'''

    with subprocess.Popen(executable, shell=True,
                          stderr=subprocess.PIPE).stderr as pipe:
        lines = b"".join(pipe.readlines())

    if IS_PYTHON3:
        lines = lines.decode('ascii')
    try:
        x = re.search(r"Version:\s+(\S+)", lines).groups()[0]
    except AttributeError:
        raise ValueError("could not get version from %s" % lines)
    return x


class SamtoolsTest(unittest.TestCase):

    '''test samtools command line commands and compare
    against pysam commands.

    Tests fail, if the output is not binary identical.
    '''

    requisites = [
        "ex1.fa", "ex1.fa.fai",
        "ex1.sam.gz",
        "ex1.bam", "ex1.bam.bai",
        "ex1.sam",
        "ex1.sam",
        "ex2.bam",
        "ex2.sam",
        "ex1.bed"]

    # a list of statements to test
    # should contain at least one %(out)s component indicating
    # an output file.
    statements = [
        "view ex1.bam > %(out)s_ex1.view",
        "view -c ex1.bam > %(out)s_ex1.count",
        # ("view -bT ex1.fa -o %(out)s_ex1.view2 ex1.sam",
        "sort ex1.bam -o %(out)s_ex1.sort.bam",
        "mpileup ex1.bam > %(out)s_ex1.pileup",
        #"depth ex1.bam > %(out)s_ex1.depth",
        # TODO: issues with file naming
        # "faidx ex1.fa; %(out)s_ex1.fa.fai",
        "index ex1.bam %(out)s_ex1.bam.fai",
        "index -@2 ex1.bam %(out)s_ex1.bam.fai",
        "idxstats ex1.bam > %(out)s_ex1.idxstats",
        "fixmate ex1.bam %(out)s_ex1.fixmate.bam",
        "flagstat ex1.bam > %(out)s_ex1.flagstat",
        # Fails python 3.3 on linux, passes on OsX and when
        # run locally
        "calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam",
        # use -s option, otherwise the following error in samtools 1.2:
        # Samtools-htslib-API: bam_get_library() not yet implemented
        # causes downstream problems
        # TODO: The following cause subsequent commands to fail
        # unknow option
        # "rmdup -s ex1.bam %(out)s_ex1.rmdup.bam",
        # "merge -f %(out)s_ex1.merge.bam ex1.bam ex1.bam",
        "reheader ex2.sam ex1.bam > %(out)s_ex1.reheader.bam",
        "cat -o %(out)s_ex1.cat.bam ex1.bam ex1.bam",
        "targetcut ex1.bam > %(out)s_ex1.targetcut",
        "phase ex1.bam > %(out)s_ex1.phase",
        #"view -bt ex1.fa.fai -o %(out)s_ex1.bam ex1.sam.gz",
        #"bam2fq ex1.bam > %(out)s_ex1.bam2fq",
        # TODO: not the same
        # "pad2unpad -T ex1.fa ex2.bam > %(out)s_ex2.unpad",
        # TODO: command line option problem
        # "bamshuf ex1.bam -O --output-fmt SAM > %(out)s_ex1.bamshuf.sam",
        # "collate ex1.bam %(out)s_ex1.collate",
        "bedcov ex1.bed ex1.bam > %(out)s_ex1.bedcov",
        "stats ex1.bam > %(out)s_ex1.stats",
        "dict ex1.bam > %(out)s_ex1.dict",
        # TODO: not the same
        # ("addreplacerg -r 'RG\tID:ga\tSM:hs' ex1.bam > %(out)s_ex1.addreplacerg",
    ]

    map_command = {
        "import": "samimport"}

    executable = "samtools"

    module = pysam.samtools

    def check_version(self):

        samtools_version = get_version(self.executable)

        def _r(s):
            # patch - remove any of the alpha/beta suffixes, i.e., 0.1.12a ->
            # 0.1.12
            if s.count('-') > 0:
                s = s[0:s.find('-')]
            return re.sub("[^0-9.]", "", s)

        if _r(samtools_version) != _r(pysam.__samtools_version__):
            warnings.warn(
                "versions of pysam.%s and %s differ: %s != %s" %
                (self.executable,
                 self.executable,
                 pysam.__samtools_version__,
                 samtools_version))

    def setUp(self):
        '''setup tests.

        For setup, all commands will be run before the first test is
        executed. Individual tests will then just compare the output
        files.

        '''
        self.check_version()

        self.workdir = os.path.join(WORKDIR, "samtools_test")
        
        if not os.path.exists(self.workdir):
            os.makedirs(self.workdir)

        for f in self.requisites:
            shutil.copy(os.path.join(BAM_DATADIR, f),
                        os.path.join(self.workdir, f))

        self.savedir = os.getcwd()
        os.chdir(self.workdir)

        return

    def get_command(self, statement, map_to_internal=True):
        """return samtools command from statement"""
        parts = statement.split(" ")
        command = parts[0]
        if map_to_internal:
            return self.map_command.get(command, command)
        else:
            return command

    def check_statement(self, statement):

        parts = statement.split(" ")
        r_samtools = {"out": self.executable}
        r_pysam = {"out": "pysam"}

        command = self.get_command(statement)

        # self.assertTrue(command in pysam.SAMTOOLS_DISPATCH)

        targets = [x for x in parts if "%(out)s" in x]
        samtools_targets = [x % r_samtools for x in targets]
        pysam_targets = [x % r_pysam for x in targets]

        pysam_method = getattr(self.module, command)

        # run samtools
        full_statement = re.sub(r"%\(out\)s", self.executable, statement)
        run_command(" ".join((self.executable, full_statement)))
        # sys.stdout.write("%s %s ok" % (command, self.executable))

        # run pysam
        if ">" in statement:
            assert parts[-2] == ">"
            parts = parts[:-2]

        # avoid interpolation to preserve string quoting, tab chars, etc.
        pysam_parts = [re.sub(r"%\(out\)s", "pysam", x) for x in parts[1:]]
        output = pysam_method(*pysam_parts,
                              raw=True,
                              catch_stdout=True)
        # sys.stdout.write(" pysam ok\n")
        if ">" in statement:
            with open(pysam_targets[-1], "wb") as outfile:
                if output is not None:
                    outfile.write(force_bytes(output))
        for samtools_target, pysam_target in zip(samtools_targets,
                                                 pysam_targets):
            if os.path.isdir(samtools_target):
                samtools_files = glob.glob(os.path.join(
                    samtools_target, "*"))
                pysam_files = glob.glob(os.path.join(pysam_target, "*"))
                self.assertEqual(len(samtools_files), len(pysam_files))
                # need to be able to exclude files like README, etc.
                continue
            else:
                samtools_files = [samtools_target]
                pysam_files = [pysam_target]

            for s, p in zip(samtools_files, pysam_files):
                binary_equal = checkBinaryEqual(s, p)
                error_msg = "%s failed: files %s and %s are not the same" % (
                    command, s, p)
                if binary_equal:
                    continue
                elif s.endswith(".bam"):
                    self.assertTrue(
                        check_samtools_view_equal(
                            s, p, without_header=True),
                        error_msg)
                else:
                    check_lines_equal(
                        self, s, p,
                        filter_f=lambda x: x.startswith("#"),
                        msg=error_msg)

    def testStatements(self):
        for statement in self.statements:
            command = self.get_command(statement, map_to_internal=False)
            # bam2fq differs between version 1.5 and 1.6 - reenable if
            # bioconda samtools will be available.
            if command in ("bedcov", "stats", "dict", "bam2fq"):
                continue

            if (command == "calmd" and
                    list(sys.version_info[:2]) == [3, 3]):
                # skip calmd test, fails only on python 3.3.5
                # in linux (empty output). Works in OsX and passes
                # for 3.4 and 3.5, see issue #293
                continue
            self.check_statement(statement)

    @unittest.skipIf(sys.platform == "darwin", "not supported, pattern does not match")
    @unittest.skipIf(not sys.stdin.isatty(), "skipping usage tests, stdin is not a tty")
    def testUsage(self):
        if self.executable == "bcftools":
            # bcftools usage messages end with exit(1)
            return

        for statement in self.statements:
            command = self.get_command(statement, map_to_internal=False)
            # ignore commands that exit or cause other failures
            # TODO: check - if reheader or phase is run in testStatements, sort fails
            # here
            if command in ("view", "sort", "bam2fq", "flagstat", "reheader",
                           "stats", "idxstats"):
                continue
            mapped_command = self.get_command(statement, map_to_internal=True)
            pysam_method = getattr(self.module, mapped_command)
            usage_msg = pysam_method.usage()
            expected = r"Usage:\s+{} {}".format(self.executable, command)
            self.assertTrue(re.search(expected, usage_msg) is not None)

    def tearDown(self):
        if os.path.exists(self.workdir):
            shutil.rmtree(self.workdir)
        os.chdir(self.savedir)


class EmptyIndexTest(unittest.TestCase):

    def testEmptyIndex(self):
        self.assertRaises(IOError, pysam.samtools.index,
                          "exdoesntexist.bam")

    def testEmptyIndexWithExtraFlag(self):
        self.assertRaises(IOError, pysam.samtools.index,
                          "-c",
                          "exdoesntexist.bam")

    def testEmptyIndexWithExtraArg(self):
        self.assertRaises(IOError, pysam.samtools.index,
                          "-c",
                          "-m",
                          "14",
                          "exdoesntexist.bam")


if sys.platform != "darwin":
    # fails with segfault with htslib 1.5 on Osx, an issue with flockfile
    # issue seems to be with repeated calls to interface

    class TestReturnType(unittest.TestCase):

        def testReturnValueString(self):
            retval = pysam.idxstats(os.path.join(BAM_DATADIR, "ex1.bam"))
            if IS_PYTHON3:
                self.assertFalse(isinstance(retval, bytes))
                self.assertTrue(isinstance(retval, str))
            else:
                self.assertTrue(isinstance(retval, bytes))
                self.assertTrue(isinstance(retval, basestring))

        def testReturnValueData(self):
            args = "-O BAM {}".format(os.path.join(BAM_DATADIR,
                                                   "ex1.bam")).split(" ")
            retval = pysam.view(*args)

            if IS_PYTHON3:
                self.assertTrue(isinstance(retval, bytes))
                self.assertFalse(isinstance(retval, str))
            else:
                self.assertTrue(isinstance(retval, bytes))
                self.assertTrue(isinstance(retval, basestring))

    class StdoutTest(unittest.TestCase):
        '''test if stdout can be redirected.'''

        def testWithRedirectedStdout(self):
            r = pysam.samtools.flagstat(
                os.path.join(BAM_DATADIR, "ex1.bam"))
            self.assertTrue(len(r) > 0)

        def testWithoutRedirectedStdout(self):
            r = pysam.samtools.flagstat(
                os.path.join(BAM_DATADIR, "ex1.bam"),
                catch_stdout=False)
            self.assertEqual(r, None)

        def testDoubleCalling(self):
            # The following would fail if there is an
            # issue with stdout being improperly caught.
            retvals = pysam.idxstats(
                os.path.join(BAM_DATADIR, "ex1.bam"))
            retvals = pysam.idxstats(
                os.path.join(BAM_DATADIR, "ex1.bam"))

        def testSaveStdout(self):
            outfile = get_temp_filename(suffix=".tsv")
            r = pysam.samtools.flagstat(
                os.path.join(BAM_DATADIR, "ex1.bam"),
                save_stdout=outfile)
            self.assertEqual(r, None)
            with open(outfile) as inf:
                r = inf.read()
            self.assertTrue(len(r) > 0)

    class PysamTest(SamtoolsTest):
        """check access to samtools command in the pysam
        main package.

        This is for backwards capability.
        """

        module = pysam

# class BcftoolsTest(SamtoolsTest):

#     requisites = [
#         "ex1.fa",
#         "ex1.vcf.gz",
#         "ex1.vcf.gz.tbi",
#     ]
#     # a list of statements to test
#     # should contain at least one %(out)s component indicating
#     # an output file.
#     statements = [
#         # "index -n ex1.vcf.gz > %(out)s_ex1.index",

#         "annotate -x ID ex1.vcf.gz > %(out)s_ex1.annotate",
#         "concat -a ex1.vcf.gz ex1.vcf.gz > %(out)s_ex1.concat",
#         "isec -p %(out)s_ex1.isec ex1.vcf.gz ex1.vcf.gz",
#         "merge --force-samples ex1.vcf.gz ex1.vcf.gz > %(out)s_ex1.norm",
#         "norm -m +both ex1.vcf.gz > %(out)s_ex1.norm",

#         # "plugin",
#         # "query -f '%CHROM\n' ex1.vcf.gz > %(out)s_ex1.query",
#         # "reheader -s A > %(out)s_ex1.reheader",
#         # "view ex1.vcf.gz > %(out)s_ex1.view",
#         # "call -m ex1.vcf.gz > %(out)s_ex1.call",
#         # bad file descriptor
#         # "consensus -f ex1.fa ex1.vcf.gz  > %(out)s_ex1.consensus"
#         # need appropriate VCF file
#         # "cnv",
#         # segfault
#         # "filter -s A ex1.vcf.gz  > %(out)s_ex1.filter",
#         # exit
#         # "gtcheck -s A ex1.vcf.gz  > %(out)s_ex1.gtcheck",
#         # segfauld, used to work wit bcftools 1.3
#         # "roh -s A ex1.vcf.gz > %(out)s_ex1.roh",
#         "stats ex1.vcf.gz > %(out)s_ex1.stats",
#     ]

#     map_command = {
#         "import": "samimport"}

#     executable = "bcftools"

#     module = pysam.bcftools


if __name__ == "__main__":
    # build data files
    print("building data files")
    subprocess.call("make -C %s" % BAM_DATADIR, shell=True)
    print("starting tests")
    unittest.main()
    print("completed tests")