def testEmptyFileVCFGZWithoutIndex(self):
with get_temp_context("tmp_testEmptyFileWithoutIndex.vcf") as fn:
with open(fn, "w"):
pass
pysam.tabix_compress(fn, fn + ".gz", force=True)
self.assertRaises(ValueError, pysam.VariantFile, fn + ".gz")
def testEmptyFileVCFGZWithIndex(self):
with get_temp_context("tmp_testEmptyFile.vcf") as fn:
with open(fn, "w"):
pass
# tabix_index will automatically compress
pysam.tabix_index(fn, preset="vcf", force=True)
self.assertRaises(ValueError, pysam.VariantFile, fn + ".gz")
def test_vcf_with_tbi_index(self):
with get_temp_context("tmp_fn.vcf") as fn:
shutil.copyfile(self.vcf_filename, fn)
pysam.tabix_index(fn, preset="vcf", force=True)
self.assertTrue(os.path.exists(fn + ".gz" + ".tbi"))
self.assertFalse(os.path.exists(fn + ".gz" + ".csi"))
with pysam.VariantFile(fn + ".gz") as inf:
self.assertEqual(len(list(inf.fetch("20"))), 3)
def test_vcf_with_tbi_index(self):
with get_temp_context("tmp_fn.vcf") as fn:
shutil.copyfile(self.vcf_filename, fn)
pysam.tabix_index(fn, preset="vcf", force=True)
self.assertTrue(os.path.exists(fn + ".gz" + ".tbi"))
self.assertFalse(os.path.exists(fn + ".gz" + ".csi"))
with pysam.VariantFile(fn + ".gz") as inf:
self.assertEqual(len(list(inf.fetch("20"))), 3)
def test_bcf_with_prebuilt_csi(self):
with get_temp_context("tmp_fn.bcf") as fn:
shutil.copyfile(self.bcf_filename, fn)
shutil.copyfile(self.bcf_filename + ".csi", fn + ".csi")
self.assertTrue(os.path.exists(fn + ".csi"))
self.assertFalse(os.path.exists(fn + ".tbi"))
with pysam.VariantFile(fn) as inf:
self.assertEqual(len(list(inf.fetch("20"))), 3)
def test_bcf_with_prebuilt_csi(self):
with get_temp_context("tmp_fn.bcf") as fn:
shutil.copyfile(self.bcf_filename, fn)
shutil.copyfile(self.bcf_filename + ".csi", fn + ".csi")
self.assertTrue(os.path.exists(fn + ".csi"))
self.assertFalse(os.path.exists(fn + ".tbi"))
with pysam.VariantFile(fn) as inf:
self.assertEqual(len(list(inf.fetch("20"))), 3)
def testEmptyFileVCFGZWithoutIndex(self):
with get_temp_context("tmp_testEmptyFileWithoutIndex.vcf") as fn:
with open(fn, "w"):
pass
pysam.tabix_compress(fn,
fn + ".gz",
force=True)
self.assertRaises(ValueError, pysam.VariantFile, fn + ".gz")
def testEmptyFileVCFGZWithIndex(self):
with get_temp_context("tmp_testEmptyFile.vcf") as fn:
with open(fn, "w"):
pass
# tabix_index will automatically compress
pysam.tabix_index(fn,
preset="vcf",
force=True)
self.assertRaises(ValueError, pysam.VariantFile, fn + ".gz")
def test_bcf_with_tbi_index_will_produce_csi(self):
with get_temp_context("tmp_fn.bcf") as fn:
shutil.copyfile(self.bcf_filename, fn)
pysam.tabix_index(fn, preset="bcf", force=True, csi=False)
self.assertTrue(os.path.exists(fn + ".csi"))
self.assertEqual(read_index_header(fn + ".csi"), b"CSI\1")
self.assertFalse(os.path.exists(fn + ".tbi"))
with pysam.VariantFile(fn) as inf:
self.assertEqual(len(list(inf.fetch("20"))), 3)
def testNegativeIntegersWrittenToFile(self):
r = self.build_read()
x = -2
r.tags = [("XD", x)]
with get_temp_context("negative_integers.bam") as fn:
with pysam.AlignmentFile(fn,
"wb",
referencenames=("chr1", ),
referencelengths=(1000, )) as outf:
outf.write(r)
with pysam.AlignmentFile(fn) as inf:
r = next(inf)
self.assertEqual(r.tags, [("XD", x)])
def testNegativeIntegersWrittenToFile(self):
r = self.build_read()
x = -2
r.tags = [("XD", x)]
with get_temp_context("negative_integers.bam") as fn:
with pysam.AlignmentFile(fn,
"wb",
referencenames=("chr1",),
referencelengths=(1000,)) as outf:
outf.write(r)
with pysam.AlignmentFile(fn) as inf:
r = next(inf)
self.assertEqual(r.tags, [("XD", x)])
def testEmptyFileVCFFromPath(self):
with get_temp_context("tmp_testEmptyFile.vcf") as fn:
with open(fn, "w"):
pass
self.assertRaises(ValueError, pysam.VariantFile, Path(fn))
def testEmptyFileVCFFromPath(self):
with get_temp_context("tmp_testEmptyFile.vcf") as fn:
with open(fn, "w"):
pass
self.assertRaises(ValueError, pysam.VariantFile,
Path(fn))
