Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
parameter.
:param stream source: The file-like object containing the text.
:param bool strict: If True, require strict tab delimiting (default). If
False, a relaxed whitespace splitting algorithm is used.
:param string encoding: Encoding used for text representation.
:param bool base64_metadata: If True, metadata is encoded using Base64
encoding; otherwise, as plain text.
:param PopulationTable table: If specified write into this table. If not,
create a new :class:`.PopulationTable` instance.
"""
sep = None
if strict:
sep = "\t"
if table is None:
table = tables.PopulationTable()
# Read the header and find the indexes of the required fields.
header = source.readline().strip("\n").split(sep)
metadata_index = header.index("metadata")
for line in source:
tokens = line.split(sep)
if len(tokens) >= 1:
metadata = tokens[metadata_index].encode(encoding)
if base64_metadata:
metadata = base64.b64decode(metadata)
table.add_row(metadata=metadata)
return table
parameter.
:param stream source: The file-like object containing the text.
:param bool strict: If True, require strict tab delimiting (default). If
False, a relaxed whitespace splitting algorithm is used.
:param string encoding: Encoding used for text representation.
:param bool base64_metadata: If True, metadata is encoded using Base64
encoding; otherwise, as plain text.
:param NodeTable table: If specified write into this table. If not,
create a new :class:`.NodeTable` instance.
"""
sep = None
if strict:
sep = "\t"
if table is None:
table = tables.NodeTable()
# Read the header and find the indexes of the required fields.
header = source.readline().strip("\n").split(sep)
is_sample_index = header.index("is_sample")
time_index = header.index("time")
population_index = None
individual_index = None
metadata_index = None
try:
population_index = header.index("population")
except ValueError:
pass
try:
individual_index = header.index("individual")
except ValueError:
pass
try:
parameter.
:param stream source: The file-like object containing the text.
:param bool strict: If True, require strict tab delimiting (default). If
False, a relaxed whitespace splitting algorithm is used.
:param string encoding: Encoding used for text representation.
:param bool base64_metadata: If True, metadata is encoded using Base64
encoding; otherwise, as plain text.
:param NodeTable table: If specified write into this table. If not,
create a new :class:`.NodeTable` instance.
"""
sep = None
if strict:
sep = "\t"
if table is None:
table = tables.NodeTable()
# Read the header and find the indexes of the required fields.
header = source.readline().strip("\n").split(sep)
is_sample_index = header.index("is_sample")
time_index = header.index("time")
population_index = None
individual_index = None
metadata_index = None
try:
population_index = header.index("population")
except ValueError:
pass
try:
individual_index = header.index("individual")
except ValueError:
pass
try:
:ref:`edge table definition ` section for the
required properties of the contents.
See :func:`.load_text` for a detailed explanation of the ``strict`` parameter.
:param stream source: The file-like object containing the text.
:param bool strict: If True, require strict tab delimiting (default). If
False, a relaxed whitespace splitting algorithm is used.
:param EdgeTable table: If specified, write the edges into this table. If
not, create a new :class:`.EdgeTable` instance and return.
"""
sep = None
if strict:
sep = "\t"
if table is None:
table = tables.EdgeTable()
header = source.readline().strip("\n").split(sep)
left_index = header.index("left")
right_index = header.index("right")
parent_index = header.index("parent")
children_index = header.index("child")
for line in source:
tokens = line.split(sep)
if len(tokens) >= 4:
left = float(tokens[left_index])
right = float(tokens[right_index])
parent = int(tokens[parent_index])
children = tuple(map(int, tokens[children_index].split(",")))
for child in children:
table.add_row(left=left, right=right, parent=parent, child=child)
return table
parameter.
:param stream source: The file-like object containing the text.
:param bool strict: If True, require strict tab delimiting (default). If
False, a relaxed whitespace splitting algorithm is used.
:param string encoding: Encoding used for text representation.
:param bool base64_metadata: If True, metadata is encoded using Base64
encoding; otherwise, as plain text.
:param IndividualTable table: If specified write into this table. If not,
create a new :class:`.IndividualTable` instance.
"""
sep = None
if strict:
sep = "\t"
if table is None:
table = tables.IndividualTable()
# Read the header and find the indexes of the required fields.
header = source.readline().strip("\n").split(sep)
flags_index = header.index("flags")
location_index = None
metadata_index = None
try:
location_index = header.index("location")
except ValueError:
pass
try:
metadata_index = header.index("metadata")
except ValueError:
pass
for line in source:
tokens = line.split(sep)
if len(tokens) >= 1: