def __call__(self, *args, **kwargs):
"""execute a samtools command.
Keyword arguments:
catch_stdout -- redirect stdout from the samtools command and return as variable (default True)
raw -- ignore any parsers associated with this samtools command.
"""
retval, stderr, stdout = _pysam_dispatch(
self.collection, self.dispatch, args, catch_stdout=kwargs.get("catch_stdout", True)
)
if retval:
raise SamtoolsError(
"%s returned with error %i: "
"stdout=%s, stderr=%s" % (self.collection, retval, "\n".join(stdout), "\n".join(stderr))
)
self.stderr = stderr
# call parser for stdout:
if not kwargs.get("raw") and stdout and self.parsers:
for options, parser in self.parsers:
for option in options:
if option not in args:
break
else:
return parser(stdout)
return stdout
def __call__(self, *args, **kwargs):
'''execute a samtools command.
Keyword arguments:
catch_stdout -- redirect stdout from the samtools command and return as variable (default True)
raw -- ignore any parsers associated with this samtools command.
'''
retval, stderr, stdout = _pysam_dispatch(self.collection,
self.dispatch,
args,
catch_stdout=kwargs.get(
"catch_stdout", True))
if retval:
raise SamtoolsError("%s returned with error %i: "
"stdout=%s, stderr=%s" %
(self.collection, retval, "\n".join(stdout),
"\n".join(stderr)))
self.stderr = stderr
# call parser for stdout:
if not kwargs.get("raw") and stdout and self.parsers:
for options, parser in self.parsers:
for option in options:
if option not in args:
break
else:
return parser(stdout)
return stdout
def __call__(self, *args, **kwargs):
'''execute a samtools command.
Keyword arguments:
catch_stdout -- redirect stdout from the samtools command and
return as variable (default True)
save_stdout -- redirect stdout to a filename.
raw -- ignore any parsers associated with this samtools command.
split_lines -- return stdout (if catch_stdout is True and stderr
as a list of strings.
'''
retval, stderr, stdout = _pysam_dispatch(
self.collection,
self.dispatch,
args,
catch_stdout=kwargs.get("catch_stdout", True),
save_stdout=kwargs.get("save_stdout", None))
if kwargs.get("split_lines", False):
stdout = stdout.splitlines()
if stderr:
stderr = stderr.splitlines()
if retval:
raise SamtoolsError(
"%s returned with error %i: "
"stdout=%s, stderr=%s" %
(self.collection,
retval,
stdout,
stderr))
self.stderr = stderr
# call parser for stdout:
if not kwargs.get("raw") and stdout and self.parsers:
for options, parser in self.parsers:
for option in options:
if option not in args:
break
else:
return parser(stdout)
return stdout
