def __call__(self, *args, **kwargs):
'''execute a samtools command
'''
retval, stderr, stdout = csamtools._samtools_dispatch(
self.dispatch, args)
if retval:
raise SamtoolsError('csamtools returned with error %i: %s' %
(retval, "\n".join(stderr)))
self.stderr = stderr
# samtools commands do not propagate the return code correctly.
# I have thus added this patch to throw if there is output on stderr.
# Note that there is sometimes output on stderr that is not an error,
# for example: [sam_header_read2] 2 sequences loaded.
# Ignore messages like these
stderr = [ x for x in stderr \
if not (x.startswith( "[sam_header_read2]" ) or \
x.startswith("[bam_index_load]") or \
x.startswith("[bam_sort_core]") or \
x.startswith("[samopen] SAM header is present") )
]
if stderr: raise SamtoolsError("\n".join(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
'''
retval, stderr, stdout = csamtools._samtools_dispatch(
self.dispatch, args)
if retval:
raise SamtoolsError(
'csamtools returned with error %i: %s' %
(retval, "\n".join(stderr)))
self.stderr = stderr
# samtools commands do not propagate the return code correctly.
# I have thus added this patch to throw if there is output on stderr.
# Note that there is sometimes output on stderr that is not an error,
# for example: [sam_header_read2] 2 sequences loaded.
# Ignore messages like these
stderr = [x for x in stderr
if not (x.startswith("[sam_header_read2]") or
x.startswith("[bam_index_load]") or
x.startswith("[bam_sort_core]") or
x.startswith("[samopen] SAM header is present"))
]
if stderr:
raise SamtoolsError("\n".join(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 = csamtools._samtools_dispatch(
self.dispatch, args, catch_stdout=kwargs.get("catch_stdout", True))
if retval:
raise SamtoolsError(
'csamtools returned with error %i: %s' %
(retval, "\n".join(stderr)))
self.stderr = stderr
# Uncommented for samtools 1.2
# # samtools commands do not propagate the return code correctly.
# # I have thus added this patch to throw if there is output on stderr.
# # Note that there is sometimes output on stderr that is not an error,
# # for example: [sam_header_read2] 2 sequences loaded.
# # Ignore messages like these
# stderr = [x for x in stderr
# if not (x.startswith("[sam_header_read2]") or
# x.startswith("[bam_index_load]") or
# x.startswith("[bam_sort_core]") or
# x.startswith("[samopen] SAM header is present"))]
# if stderr:
# raise SamtoolsError("\n".join(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 = csamtools._samtools_dispatch(
self.dispatch, args, catch_stdout=kwargs.get("catch_stdout", True))
if retval:
raise SamtoolsError('csamtools returned with error %i: %s' %
(retval, "\n".join(stderr)))
self.stderr = stderr
# Uncommented for samtools 1.2
# # samtools commands do not propagate the return code correctly.
# # I have thus added this patch to throw if there is output on stderr.
# # Note that there is sometimes output on stderr that is not an error,
# # for example: [sam_header_read2] 2 sequences loaded.
# # Ignore messages like these
# stderr = [x for x in stderr
# if not (x.startswith("[sam_header_read2]") or
# x.startswith("[bam_index_load]") or
# x.startswith("[bam_sort_core]") or
# x.startswith("[samopen] SAM header is present"))]
# if stderr:
# raise SamtoolsError("\n".join(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 usage(self):
'''return the samtools usage information for this command'''
retval, stderr, stdout = csamtools._samtools_dispatch(self.dispatch)
return "".join(stderr)
def usage(self):
'''return the samtools usage information for this command'''
retval, stderr, stdout = csamtools._samtools_dispatch(
self.dispatch)
return "".join(stderr)
