mirror of
https://github.com/biopython/biopython.git
synced 2025-10-21 14:33:47 +08:00
68e3c989d9
$ ruff --fix --select PIE790 BioSQL/ Bio/ Doc/examples/ Tests/ Scripts/ Found 62 errors (62 fixed, 0 remaining). Then re-ran black.
118 lines
3.9 KiB
Python
118 lines
3.9 KiB
Python
# Copyright 2014 Joe Cora.
|
|
# Revisions copyright 2017 Peter Cock.
|
|
# All rights reserved.
|
|
#
|
|
# This file is part of the Biopython distribution and governed by your
|
|
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
|
|
# Please see the LICENSE file that should have been included as part of this
|
|
# package.
|
|
|
|
"""Objects to represent NEXUS standard data type matrix coding."""
|
|
|
|
|
|
class NexusError(Exception):
|
|
"""Provision for the management of Nexus exceptions."""
|
|
|
|
|
|
class StandardData:
|
|
"""Create a StandardData iterable object.
|
|
|
|
Each coding specifies t [type] => (std [standard], multi [multistate] or
|
|
uncer [uncertain]) and d [data]
|
|
"""
|
|
|
|
def __init__(self, data):
|
|
"""Initialize the class."""
|
|
self._data = []
|
|
self._current_pos = 0
|
|
|
|
# Enforce string data requirement
|
|
if not isinstance(data, str):
|
|
raise NexusError(
|
|
"The coding data given to a StandardData object should be a string"
|
|
)
|
|
|
|
# Transfer each coding to a position within a sequence
|
|
multi_coding = False
|
|
uncertain_coding = False
|
|
coding_list = {"t": "std", "d": []}
|
|
|
|
for pos, coding in enumerate(data):
|
|
# Check if in a multiple coded or uncertain character
|
|
if multi_coding:
|
|
# End multicoding if close parenthesis
|
|
if coding == ")":
|
|
multi_coding = False
|
|
else:
|
|
# Add current coding to list and advance to next coding
|
|
coding_list["d"].append(coding)
|
|
continue
|
|
elif uncertain_coding:
|
|
# End multicoding if close parenthesis
|
|
if coding == "}":
|
|
uncertain_coding = False
|
|
else:
|
|
# Add current coding to list and advance to next coding
|
|
coding_list["d"].append(coding)
|
|
continue
|
|
else:
|
|
# Check if a multiple coded or uncertain character is starting
|
|
if coding == "(":
|
|
multi_coding = True
|
|
coding_list["t"] = "multi"
|
|
continue
|
|
elif coding == "{":
|
|
uncertain_coding = True
|
|
coding_list["t"] = "uncer"
|
|
continue
|
|
elif coding in [")", "}"]:
|
|
raise NexusError(
|
|
"Improper character %s at position %i of a coding sequence."
|
|
% (coding, pos)
|
|
)
|
|
else:
|
|
coding_list["d"].append(coding)
|
|
|
|
# Add character coding to data
|
|
self._data.append(coding_list.copy())
|
|
coding_list = {"t": "std", "d": []}
|
|
|
|
def __len__(self):
|
|
"""Return the length of the coding, use len(my_coding)."""
|
|
return len(self._data)
|
|
|
|
def __getitem__(self, arg):
|
|
"""Pull out child by index."""
|
|
return self._data[arg]
|
|
|
|
def __iter__(self):
|
|
"""Iterate over the items."""
|
|
return self
|
|
|
|
def __next__(self):
|
|
"""Return next item."""
|
|
try:
|
|
return_coding = self._data[self._current_pos]
|
|
except IndexError:
|
|
self._current_pos = 0
|
|
raise StopIteration from None
|
|
else:
|
|
self._current_pos += 1
|
|
return return_coding
|
|
|
|
def raw(self):
|
|
"""Return the full coding as a python list."""
|
|
return self._data
|
|
|
|
def __str__(self):
|
|
"""Return the full coding as a python string, use str(my_coding)."""
|
|
str_return = ""
|
|
for coding in self._data:
|
|
if coding["t"] == "multi":
|
|
str_return += "(" + "".join(coding["d"]) + ")"
|
|
elif coding["t"] == "uncer":
|
|
str_return += "{" + "".join(coding["d"]) + "}"
|
|
else:
|
|
str_return += coding["d"][0]
|
|
return str_return
|