def pdfcomments(infilename: str, outfilename: Optional[str] = None) -> int:
severities = load_comments(infilename)
if outfilename is None:
outfilename = extsep.join([Path(infilename).stem, OUT_EXT])
save_comments(severities, outfilename)
return EX_OK
def get_show_keys():
'''
Gets contents of show_keys result file
'''
filename = ospath.join(
RESULT_DIR,
extsep.join(['show_keys', 'txt', ]),
)
with open(filename) as fhandle:
return fhandle.read()
def joinext(root, ext):
"""
Roughly the reverse of os.path.splitext.
:type root: string
:param root: part of the filename before the extension
:type root: string
:param ext: the extension
:rtype: string
:returns: ``root`` joined with ``ext`` separated by a single ``os.extsep``
"""
return extsep.join([root.rstrip(extsep), ext.lstrip(extsep)])
def get_test_result(key):
'''
Read data and result for given key
'''
filename = ospath.join(
RESULT_DIR,
extsep.join([key, 'yaml', ]),
)
with open(filename) as fhandle:
result = load(fhandle)
return result
def get_show_keys():
'''
Gets contents of show_keys result file
'''
filename = ospath.join(
RESULT_DIR,
extsep.join([
'show_keys',
'txt',
]),
)
with open(filename) as fhandle:
return fhandle.read()
def test_module(subclass, directory=False):
'''Executes subclass and outputs data
:param subclass: key to subclass under test
:param directory: optional - indicates that input data is
a directory
'''
subclass.read()
data = ospath.join(SUBDIR, 'data')
result = ospath.join(SUBDIR, 'result')
# make raw data directory
for i in (data, result):
try:
mkdir(i)
except OSError as ex:
if ex.errno != errno.EEXIST:
raise
# write raw data for later inspection
# ignore if input is a directory
# (PidFd class) or no data found
if not directory:
try:
with open(
ospath.join(data, subclass.key), 'wt'
) as fd:
fd.write(subclass.data)
fd.write('\n')
except (AttributeError, TypeError):
pass
# write result dictionary for later inspection
with open(
extsep.join([
ospath.join(result, subclass.key),
'yaml',
]),
'wt'
) as fd:
yaml.dump(
subclass.normalize(),
stream=fd,
indent=2,
width=80,
default_flow_style=False
)
def get_test_result(key):
'''
Read data and result for given key
'''
filename = ospath.join(
RESULT_DIR,
extsep.join([
key,
'yaml',
]),
)
with open(filename) as fhandle:
result = load(fhandle)
return result
def write_result(key, result):
'''
Sometimes we want to actially write the result
dictionary
'''
filename = ospath.join(
RESULT_DIR,
extsep.join([key, 'yaml', ]),
)
with open(filename) as fhandle:
result = dump(
result,
fhandle,
indent=2,
width=80,
default_flow_style=False
)
def write_result(key, result):
'''
Sometimes we want to actially write the result
dictionary
'''
filename = ospath.join(
RESULT_DIR,
extsep.join([
key,
'yaml',
]),
)
with open(filename) as fhandle:
result = dump(result,
fhandle,
indent=2,
width=80,
default_flow_style=False)
def run():
parser = argparse.ArgumentParser(usage=__doc__)
parser.add_argument('--hla-dir', required=True)
parser.add_argument('--maf-dir', required=True)
args = parser.parse_args()
hla_dir_out = args.hla_dir + "_cleaned"
maf_dir_out = args.maf_dir + "_cleaned"
shutil.rmtree(hla_dir_out, ignore_errors=True)
shutil.rmtree(maf_dir_out, ignore_errors=True)
makedirs(hla_dir_out)
makedirs(maf_dir_out)
maf_set = set()
both_set = set()
maf_exts = []
for maf_filename in listdir(args.maf_dir):
maf_parts = maf_filename.split(extsep)
if "maf" in maf_parts:
maf_set.add(maf_parts[0])
maf_exts.append(extsep + extsep.join(maf_parts[1:]))
for hla_filename in listdir(args.hla_dir):
hla_basename, hla_ext = path.splitext(hla_filename)
hla_stripped_basename = hla_basename[:NUM_CHARS_HLA]
hla_stripped_filename = hla_stripped_basename + hla_ext
if ".hla" == hla_ext and hla_stripped_basename in maf_set:
both_set.add(hla_stripped_basename)
hla_filepath = path.join(args.hla_dir, hla_filename)
lines = [strip_info(line) for line in open(hla_filepath)]
hla_filepath_new = path.join(hla_dir_out,
hla_stripped_filename)
with open(hla_filepath_new, 'a') as nf:
output = '\n'.join(lines)
nf.write(output)
maf_dirpath = path.abspath(args.maf_dir)
maf_dirpath_out = path.abspath(maf_dir_out)
for basename in both_set:
maf_filepath_original = path.join(maf_dirpath, basename) + maf_exts[0]
maf_basepath = path.join(maf_dirpath_out, basename)
maf_filepath = maf_basepath + maf_exts[0]
maf_filepath_new = maf_basepath + ".maf"
shutil.copyfile(maf_filepath_original, maf_filepath)
rename(maf_filepath, maf_filepath_new)
def get_output_filename (self):
return self.output \
if self.output is not None \
else extsep.join((self.task_name.replace(' ', extsep), 'csv'))
def extjoin(*args):
return extsep.join(args)
