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'''
compile_test.py - check pyximport functionality with pysam
==========================================================
test script for checking if compilation against
pysam and tabix works.
'''
# clean up previous compilation
import os
import platform
import pytest
import pysam
from TestUtils import make_data_files, BAM_DATADIR, CBCF_DATADIR, TABIX_DATADIR
def setUpModule():
make_data_files(BAM_DATADIR)
make_data_files(CBCF_DATADIR)
make_data_files(TABIX_DATADIR)
try:
os.unlink('tests/_compile_test.c')
os.unlink('tests/_compile_test.pyxbldc')
except OSError:
pass
NO_PYXIMPORT = False
try:
import pyximport
pyximport.install(build_in_temp=False)
import _compile_test
except:
NO_PYXIMPORT = True
@pytest.mark.skipif(NO_PYXIMPORT, reason="no pyximport")
def test_bam():
input_filename = os.path.join(BAM_DATADIR, "ex1.bam")
nread = _compile_test.testCountBAM(
pysam.Samfile(input_filename))
assert nread == 3270
@pytest.mark.skipif(NO_PYXIMPORT, reason="no pyximport")
def test_gtf():
input_filename = os.path.join(TABIX_DATADIR, "example.gtf.gz")
nread = _compile_test.testCountGTF(
pysam.Tabixfile(input_filename))
assert nread == 237
@pytest.mark.skipif(
platform.architecture()[0] != '64bit',
reason="64-bit specific tests"
)
class TestBinaryCompatibility:
def test_alignments(self):
fp = pysam.AlignmentFile(os.path.join(BAM_DATADIR, "ex1.bam"))
hdr = pysam.AlignmentHeader()
aln = pysam.AlignedSegment()
assert fp.__sizeof__() == 120
assert hdr.__sizeof__() == 24
assert aln.__sizeof__() == 72
def test_variants(self):
fp = pysam.VariantFile(os.path.join(CBCF_DATADIR, "example_vcf43.vcf"))
hdr = pysam.VariantHeader()
assert fp.__sizeof__() == 120
assert hdr.__sizeof__() == 32
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