def complete_check(self, fn_in, fn_out):
self.maxDiff = None
check_lines_equal(self,
fn_in,
fn_out,
sort=True,
filter_f=lambda x: x.startswith("##contig"))
os.unlink(fn_out)
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("%\(out\)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.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 complete_check(self, fn_in, fn_out):
check_lines_equal(
self, fn_in, fn_out, sort=True,
filter_f=lambda x: x.startswith("##contig"))
os.unlink(fn_out)
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.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
if s.endswith(".bam"):
self.assertTrue(
check_samtools_view_equal(
s, p, without_header=True),
error_msg)
check_lines_equal(
self, s, p,
filter_f=lambda x: x.startswith("#"),
msg=error_msg)