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import inspect
import os
import pytest
import re
from typing import TYPE_CHECKING
import pysam
import pysam.samtools
import pysam.bcftools
from TestUtils import BAM_DATADIR, make_data_files
try:
import mypy.api
except ImportError:
pytest.skip('mypy API not available', allow_module_level=True)
PREAMBLE = """
import re
from typing import TYPE_CHECKING
import pysam
import pysam.samtools
import pysam.bcftools
def typecheck(check_locals = True): pass
"""
MYPY_OPTIONS = ['--no-incremental', '--no-error-summary', '--follow-imports', 'silent']
def typecheck(check_locals: bool = True):
myframe = inspect.currentframe()
if not myframe: pytest.skip('current stack frame not available')
caller = myframe.f_back
if not caller: pytest.skip('caller stack frame not available')
code = inspect.getsource(caller)
stdout, stderr, status = mypy.api.run(MYPY_OPTIONS + ['--command', PREAMBLE + code])
assert status == 0, f'mypy failed:\n{stdout}{stderr}'
types = {}
for line in stdout.splitlines():
m = re.search(r'note: *(\w+): ([\w.]*)', line)
if m: types[m.group(1)] = m.group(2)
def _plain(s):
s = re.sub(r"<class '([^']*)'>", r'\1', s)
s = re.sub(r'builtins\.', '', s)
return s
if check_locals:
for var, vartype in types.items():
assert _plain(vartype) == _plain(repr(type(caller.f_locals[var]))), f'Incorrect type for {var!r}'
return types
def setUpModule():
make_data_files(BAM_DATADIR)
@pytest.fixture
def aln():
header = pysam.AlignmentHeader.from_references(['chr1', 'chr2'], [50000, 20000])
a = pysam.AlignedSegment(header)
a.query_name = 'read_one'
a.flag = pysam.FPAIRED | pysam.FREAD1
a.reference_id = 0
a.reference_start = 1000
a.mapping_quality = 20
a.next_reference_id = 1
a.next_reference_start = 5000
a.template_length = 0
a.cigartuples = ((pysam.CMATCH, 6), (pysam.CINS, 4), (pysam.CMATCH, 2))
a.query_sequence = 'ATGCATGCATGC'
a.query_qualities = pysam.qualitystring_to_array('abcdefghijkl')
return a
@pytest.fixture
def sam_fname():
return os.path.join(BAM_DATADIR, 'ex3.sam')
@pytest.fixture
def bam_fname():
return os.path.join(BAM_DATADIR, 'ex1.bam')
def test_AlignedSegment_is_mapped(aln: pysam.AlignedSegment) -> None:
rmap = aln.is_mapped
mmap = aln.mate_is_mapped
rfwd = aln.is_forward
mfwd = aln.mate_is_forward
if TYPE_CHECKING: reveal_locals()
types = typecheck()
def test_AlignmentHeader_get_reference_length(sam_fname: str) -> None:
inf = pysam.AlignmentFile(sam_fname)
n1 = inf.get_reference_length('chr1')
hdr = inf.header
n2 = hdr.get_reference_length('chr1')
if TYPE_CHECKING: reveal_locals()
types = typecheck()
def test_pileup_iterator_column(bam_fname: str) -> None:
inf = pysam.AlignmentFile(bam_fname)
pu = inf.pileup('chr1')
for p in pu:
pid = p.reference_id
ppos = p.reference_pos
if TYPE_CHECKING: reveal_locals()
types = typecheck(check_locals=False)
assert re.search(r'\.IteratorColumn(|All|AllRefs|Region)$', types['pu'])
assert types['p'].endswith('PileupColumn')
assert types['pid'] == 'builtins.int'
assert types['ppos'] == 'builtins.int'
def test_samtools_subcommands() -> None:
p1_samtools_faidx = pysam.samtools.faidx
p2_faidx = pysam.faidx
p3_view = pysam.view
p4_bcftools_view = pysam.bcftools.view
if TYPE_CHECKING: reveal_locals()
types = typecheck()
for var, vartype in types.items():
assert vartype.endswith('PysamDispatcher'), f'{var!r} is not a dispatcher'
|
