def testIndexPresetCompressed(self):
'''test indexing via preset.'''
pysam.tabix_compress(self.tmpfilename, self.tmpfilename + ".gz")
pysam.tabix_index(self.tmpfilename + ".gz", preset=self.preset)
checkBinaryEqual(self.tmpfilename + ".gz", self.filename)
checkBinaryEqual(self.tmpfilename + ".gz.tbi", self.filename_idx)
def testIndexPresetUncompressed(self):
'''test indexing via preset.'''
pysam.tabix_index(self.tmpfilename, preset=self.preset)
# check if uncompressed file has been removed
self.assertEqual(os.path.exists(self.tmpfilename), False)
checkBinaryEqual(self.tmpfilename + ".gz", self.filename)
checkBinaryEqual(self.tmpfilename + ".gz.tbi", self.filename_idx)
def checkCommand(self, command):
if command:
samtools_target, pysam_target = self.commands[
command][0][0], self.commands[command][1][0]
samtools_target = os.path.join(WORKDIR, samtools_target)
pysam_target = os.path.join(WORKDIR, pysam_target)
self.assertTrue(checkBinaryEqual(samtools_target, pysam_target),
"%s failed: files %s and %s are not the same" % (command, samtools_target, pysam_target))
def checkCommand(self, command):
if command:
samtools_target, pysam_target = self.commands[
command][0][0], self.commands[command][1][0]
samtools_target = os.path.join(WORKDIR, samtools_target)
pysam_target = os.path.join(WORKDIR, pysam_target)
self.assertTrue(checkBinaryEqual(samtools_target, pysam_target),
"%s failed: files %s and %s are not the same" % (command, samtools_target, pysam_target))
def check_statement(self, statement):
parts = statement.split(" ")
r_samtools = {"out": self.executable}
r_pysam = {"out": "pysam"}
command = parts[0]
command = self.map_command.get(command, command)
# 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("%\(out\)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("%\(out\)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 = outfile.write(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):
self.assertTrue(
checkBinaryEqual(s, p),
"%s failed: files %s and %s are not the same" %
(command, s, p))
def check_statement(self, statement):
parts = statement.split(" ")
r_samtools = {"out": self.executable}
r_pysam = {"out": "pysam"}
command = parts[0]
command = self.map_command.get(command, command)
# 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("%\(out\)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("%\(out\)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 = outfile.write(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):
self.assertTrue(checkBinaryEqual(s, p), "%s failed: files %s and %s are not the same" % (command, s, p))
def testCompression(self):
'''see also issue 106'''
pysam.tabix_compress(self.tmpfilename, self.tmpfilename + ".gz")
checkBinaryEqual(self.tmpfilename, self.tmpfilename + ".gz")