def __init__(self, f, fname, default_sample_id):
TextParser.__init__(self, f, fname, default_sample_id)
self.__format = None
# Metadata and comments
line = self._readline()
while len(line) > 0 and line.startswith("#"):
if line.startswith("##fileformat="):
self.__format = line[13:]
line = self._readline()
if len(line) > 0: # Header
column_indices = {}
columns = line.rstrip().split("\t")
self._col_size = len(columns)
for i, name in enumerate(columns):
name = name.lower()
if name in _COLUMNS:
column_indices[name] = i
try:
self._col_name_indices = column_indices
self._col_indices = [column_indices[name] for name in _COLUMNS]
except KeyError as ex:
raise ParserException("Header column not found: {0}".format(ex.args[0]), self._location())
else:
raise ParserException("Header not found", (self._fname))
def __init__(self, f, fname, default_sample_id):
TextParser.__init__(self, f, fname, default_sample_id)
self.__format = None
# Metadata and comments
line = self._readline()
while len(line) > 0 and line.startswith("#"):
if line.startswith("##INDIVIDUAL="):
self._default_sample_id = line[13:]
elif line.startswith("##fileformat="):
self.__format = line[13:]
line = self._readline()
if len(line) > 0: # First line
self._queue_line(line)
def __init__(self, f, fname, default_sample_id): TextParser.__init__(self, f, fname, default_sample_id)
