# propy3, formerly protpy, is a Python package to compute protein descriptors
# Copyright (C) 2012 Dongsheng Cao and Yizeng Liang, oriental-cds@163.com
# Copyright (C) 2020-2022 Martin Thoma
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; in version 2
# of the License.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor,
# Boston, MA 02110-1301, USA.
"""
This module is used for obtaining the properties of amino acids or their pairs
from the aaindex database.
"""
# Core Library
import logging
import os
import sys
from typing import Any, Dict, List, Optional, Type, cast
# Third party
import pkg_resources
# First party
from propy import AALetter
logger = logging.getLogger(__name__)
_aaindex: Dict[Any, Any] = {}
[docs]class Record:
"""Amino acid index (AAindex) Record."""
aakeys = "ARNDCQEGHILKMFPSTWYV"
def __init__(self):
self.key = None
self.desc = ""
self.ref = ""
self.authors = ""
self.title = ""
self.journal = ""
self.correlated = {}
self.index = {}
self.comment = ""
[docs] def extend(self, row: List[Optional[float]]) -> None:
"""Extend self.index by the elements of the list."""
i = len(self.index)
for x in row:
self.index[self.aakeys[i]] = x
i += 1
[docs] def get(self, aai, aaj=None, d=None):
assert aaj is None
return self.index.get(aai, d)
def __getitem__(self, aai):
return self.get(aai)
def __str__(self):
desc = self.desc.replace("\n", " ").strip()
return f"{self.__class__.__name__}({self.key}: {desc})"
[docs]class MatrixRecord(Record):
"""Matrix record for mutation matrices or pair-wise contact potentials."""
def __init__(self):
Record.__init__(self)
self.index: List[Any] = [] # type: ignore
self.rows = {}
self.cols = {}
[docs] def extend(self, row):
self.index.append(row)
def _get(self, aai, aaj):
i = self.rows[aai]
j = self.cols[aaj]
return self.index[i][j]
[docs] def get(self, aai, aaj, d=None):
try:
return self._get(aai, aaj)
except Exception as e:
logger.debug(e)
pass
try:
return self._get(aaj, aai)
except Exception as e:
logger.debug(e)
return d
def __getitem__(self, aaij):
return self.get(aaij[0], aaij[1])
[docs]def search(pattern, searchtitle=True, casesensitive=False):
"""
Search for pattern in description and title (optional) of all records and
return matched records as list. By default search case insensitive.
"""
whatcase = lambda i: i
if not casesensitive:
pattern = pattern.lower()
whatcase = lambda i: i.lower()
matches = []
for record in _aaindex.values():
if (
pattern in whatcase(record.desc)
or searchtitle
and pattern in whatcase(record.title)
):
matches.append(record)
return matches
[docs]def grep(pattern):
"""
Search for pattern in title and description of all records (case
insensitive) and print results on standard output.
"""
for record in search(pattern):
print(record)
[docs]def get(key: str):
"""Get record for key."""
if len(_aaindex) == 0:
init()
return _aaindex[key]
def _float_or_None(x) -> Optional[float]:
if x == "NA" or x == "-":
return None
return float(x)
[docs]def init(path: Optional[str] = None, index: str = "123"):
"""
Read in the aaindex files. You need to run this (once) before you can
access any records. If the files are not within the current directory, you
need to specify the correct directory path. By default all three aaindex
files are read in.
"""
index = str(index)
if path is None:
filepath = pkg_resources.resource_filename(__name__, "aaindex1")
path = os.path.dirname(filepath)
print("path =", path, file=sys.stderr)
if "1" in index:
_parse(os.path.join(path, "aaindex1"), Record)
if "2" in index:
_parse(os.path.join(path, "aaindex2"), MatrixRecord)
if "3" in index:
_parse(os.path.join(path, "aaindex3"), MatrixRecord)
[docs]def init_from_file(filename, type=Record):
_parse(filename, type)
def _parse(filename: str, rec: Type[Record], quiet: bool = True):
"""
Parse aaindex input file. `rec` must be `Record` for aaindex1 and
`MarixRecord` for aaindex2 and aaindex3.
"""
if not os.path.exists(filename):
# Core Library
from urllib.request import urlretrieve
url = (
"ftp://ftp.genome.jp/pub/db/community/aaindex/" + os.path.split(filename)[1]
)
logger.debug(f'Downloading "{url}"')
filename = urlretrieve(url, filename)[0]
logger.debug(f'Saved to "{filename}"')
f = open(filename)
current = rec()
lastkey = None
for line in f:
key = line[0:2]
if key[0] == " ":
key = lastkey # type: ignore
if key == "//":
_aaindex[current.key] = current
current = rec()
elif key == "H ":
current.key = line[2:].strip()
elif key == "R ":
current.ref += line[2:]
elif key == "D ":
current.desc += line[2:]
elif key == "A ":
current.authors += line[2:]
elif key == "T ":
current.title += line[2:]
elif key == "J ":
current.journal += line[2:]
elif key == "* ":
current.comment += line[2:]
elif key == "C ":
a = line[2:].split()
for i in range(0, len(a), 2):
current.correlated[a[i]] = float(a[i + 1])
elif key == "I ":
a = line[1:].split()
if a[0] != "A/L":
current.extend([_float_or_None(el) for el in a])
elif list(Record.aakeys) != [i[0] for i in a] + [i[-1] for i in a]:
print("Warning: wrong amino acid sequence for", current.key)
else:
try:
assert list(Record.aakeys[:10]) == [i[0] for i in a]
assert list(Record.aakeys[10:]) == [i[2] for i in a]
except Exception as e:
logger.debug(e)
print("Warning: wrong amino acid sequence for", current.key)
elif key == "M ":
current = cast(MatrixRecord, current) # TODO: is this guaranteed?
a = line[2:].split()
if a[0] == "rows":
if a[4] == "rows":
a.pop(4)
assert a[3] == "cols" and len(a) == 6
i = 0
for aa in a[2]:
current.rows[aa] = i
i += 1
i = 0
for aa in a[5]:
current.cols[aa] = i
i += 1
else:
current.extend([_float_or_None(el) for el in a])
elif not quiet:
print('Warning: line starts with "%s"' % (key))
lastkey = key
f.close()
[docs]def GetAAIndex1(name: str, path: Optional[str] = ".") -> Dict[str, float]:
"""
Get the amino acid property values from aaindex1.
Parameters
----------
name : str
name of amino acid property (e.g., KRIW790103)
Returns
-------
result : Dict[str, float]
contains the properties of 20 amino acids
Examples
--------
>>> result = GetAAIndex1("KRIW790103")
"""
init(path=path)
name = str(name)
temp = get(name.strip())
res = {}
for i in AALetter:
res[i] = temp.get(i)
return res
[docs]def GetAAIndex23(name: str, path: Optional[str] = ".") -> Dict[str, float]:
"""
Get the amino acid property values from aaindex2 and aaindex3.
Parameters
----------
name : str
name of amino acid property (e.g. TANS760101, GRAR740104)
Returns
-------
result : Dict[str, float]
contains the properties of 400 amino acid pairs
Examples
--------
>>> result = GetAAIndex23("TANS760101")
"""
init(path=path)
name = str(name)
temp = get(name.strip())
res = {}
for i in AALetter:
for j in AALetter:
res[i + j] = temp.get(i, j)
return res