# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
##############################################################################
A class used for computing different types of DNA descriptors!
You can freely use and distribute it. If you have any problem,
you could contact with us timely.
Authors: Zhijiang Yao and Dongsheng Cao.
Date: 2016.07.11
Email: gadsby@163.com and oriental-cds@163.com
##############################################################################
"""
from PyDNAutil import GetData, GeneratePhycheValue
from functools import reduce
[docs]def CheckAcc(lag, k):
"""
#################################################################
Check ACC parameter validation.
#################################################################
"""
try:
if not isinstance(lag, int) or lag <= 0:
raise ValueError("Error, parameter lag must be an int type and larger than 0.")
elif not isinstance(k, int) or lag <= 0:
raise ValueError("Error, parameter k must be an int type and larger than 0.")
except ValueError:
raise
[docs]def ReadyAcc(input_data, k, phyche_index=None, all_property=False, extra_phyche_index=None):
"""
#################################################################
Public function for get sequence_list and phyche_value.
#################################################################
"""
sequence_list = GetData(input_data)
if phyche_index is None:
phyche_index = []
if extra_phyche_index is None:
extra_phyche_index = {}
phyche_value = GeneratePhycheValue(k, phyche_index, all_property, extra_phyche_index)
return sequence_list, phyche_value
[docs]def GetDAC(input_data,**kwargs):
"""
#################################################################
Make DAC dictionary.
:param input_data: file object or sequence list.
:param phyche_index: physicochemical properties list.
:param all_property: bool, choose all physicochemical properties or not.
:param extra_phyche_index: dict, the key is the dinucleotide (string), and its corresponding value is a list.
It means user-defined phyche_index.
#################################################################
"""
if 'k' in kwargs:
k = kwargs['k']
else:
k = 2
if 'lag' in kwargs:
lag = kwargs['lag']
else:
lag = 2
if 'phyche_index' in kwargs:
phyche_index = kwargs['phyche_index']
else:
phyche_index = None
if 'all_property' in kwargs:
all_property = kwargs['all_property']
else:
all_property = False
if 'extra_phyche_index' in kwargs:
extra_phyche_index = kwargs['extra_phyche_index']
else:
extra_phyche_index = None
input_data = [input_data]
sequence_list, phyche_value = ReadyAcc(input_data, k, phyche_index, all_property, extra_phyche_index)
from PyDNAacutil import MakeACVector
vec = MakeACVector(sequence_list, lag, phyche_value, k)
dict_keys = ['DAC_%s'%i for i in range(1,len(vec[0])+1)]
res = dict(zip(dict_keys,vec[0]))
return res
[docs]def GetDCC(input_data,**kwargs):
"""
#################################################################
Make DCC vector.
:param input_data: file object or sequence list.
:param phyche_index: physicochemical properties list.
:param all_property: bool, choose all physicochemical properties or not.
:param extra_phyche_index: dict, the key is the dinucleotide (string), and its corresponding value is a list.
It means user-defined phyche_index.
#################################################################
"""
if 'k' in kwargs:
k = kwargs['k']
else:
k = 2
if 'lag' in kwargs:
lag = kwargs['lag']
else:
lag = 2
if 'phyche_index' in kwargs:
phyche_index = kwargs['phyche_index']
else:
phyche_index = None
if 'all_property' in kwargs:
all_property = kwargs['all_property']
else:
all_property = False
if 'extra_phyche_index' in kwargs:
extra_phyche_index = kwargs['extra_phyche_index']
else:
extra_phyche_index = None
input_data = [input_data]
sequence_list, phyche_value = ReadyAcc(input_data, k, phyche_index, all_property, extra_phyche_index)
from PyDNAacutil import MakeCCVector
vec = MakeCCVector(sequence_list, lag, phyche_value, k)
dict_keys = ['DCC_%s'%i for i in range(1,len(vec[0])+1)]
res = dict(zip(dict_keys,vec[0]))
return res
[docs]def GetDACC(input_data, **kwargs):
"""
#################################################################
Make DACC dictionary.
:param input_data: file object or sequence list.
:param phyche_index: physicochemical properties list.
:param all_property: bool, choose all physicochemical properties or not.
:param extra_phyche_index: dict, the key is the dinucleotide (string), and its corresponding value is a list.
It means user-defined phyche_index.
#################################################################
"""
if 'k' in kwargs:
k = kwargs['k']
else:
k = 2
if 'lag' in kwargs:
lag = kwargs['lag']
else:
lag = 2
if 'phyche_index' in kwargs:
phyche_index = kwargs['phyche_index']
else:
phyche_index = None
if 'all_property' in kwargs:
all_property = kwargs['all_property']
else:
all_property = False
if 'extra_phyche_index' in kwargs:
extra_phyche_index = kwargs['extra_phyche_index']
else:
extra_phyche_index = None
input_data = [input_data]
sequence_list, phyche_value = ReadyAcc(input_data, k, phyche_index, all_property, extra_phyche_index)
from PyDNAacutil import MakeACVector, MakeCCVector
zipped = list(zip(MakeACVector(sequence_list, lag, phyche_value, k),
MakeCCVector(sequence_list, lag, phyche_value, k)))
vec = [reduce(lambda x, y: x + y, e) for e in zipped]
dict_keys = ['DACC_%s'%i for i in range(1,len(vec[0])+1)]
res = dict(zip(dict_keys,vec[0]))
return res
[docs]def GetTAC(input_data, **kwargs):
"""
#################################################################
Make TAC dictionary.
:param input_data: file object or sequence list.
:param phyche_index: physicochemical properties list.
:param all_property: bool, choose all physicochemical properties or not.
:param extra_phyche_index: dict, the key is the dinucleotide (string), and its corresponding value is a list.
It means user-defined phyche_index.
#################################################################
"""
if 'k' in kwargs:
k = kwargs['k']
else:
k = 3
if 'lag' in kwargs:
lag = kwargs['lag']
else:
lag = 2
if 'phyche_index' in kwargs:
phyche_index = kwargs['phyche_index']
else:
phyche_index = None
if 'all_property' in kwargs:
all_property = kwargs['all_property']
else:
all_property = False
if 'extra_phyche_index' in kwargs:
extra_phyche_index = kwargs['extra_phyche_index']
else:
extra_phyche_index = None
input_data = [input_data]
sequence_list, phyche_value = ReadyAcc(input_data, k, phyche_index, all_property, extra_phyche_index)
from PyDNAacutil import MakeACVector
vec = MakeACVector(sequence_list, lag, phyche_value, k)
dict_keys = ['TAC_%s'%i for i in range(1,len(vec[0])+1)]
res = dict(zip(dict_keys,vec[0]))
return res
[docs]def GetTCC( input_data,**kwargs):
"""
#################################################################
Make TCC dictionary.
:param input_data: file object or sequence list.
:param phyche_index: physicochemical properties list.
:param all_property: bool, choose all physicochemical properties or not.
:param extra_phyche_index: dict, the key is the dinucleotide (string), and its corresponding value is a list.
It means user-defined phyche_index.
#################################################################
"""
if 'k' in kwargs:
k = kwargs['k']
else:
k = 3
if 'lag' in kwargs:
lag = kwargs['lag']
else:
lag = 2
if 'phyche_index' in kwargs:
phyche_index = kwargs['phyche_index']
else:
phyche_index = None
if 'all_property' in kwargs:
all_property = kwargs['all_property']
else:
all_property = False
if 'extra_phyche_index' in kwargs:
extra_phyche_index = kwargs['extra_phyche_index']
else:
extra_phyche_index = None
input_data = [input_data]
sequence_list, phyche_value = ReadyAcc(input_data, k, phyche_index, all_property, extra_phyche_index)
from PyDNAacutil import MakeCCVector
vec = MakeCCVector(sequence_list, lag, phyche_value, k)
dict_keys = ['TCC_%s'%i for i in range(1,len(vec[0])+1)]
res = dict(zip(dict_keys,vec[0]))
return res
[docs]def GetTACC(input_data,**kwargs):
"""
#################################################################
Make TACC dictionary.
:param input_data: file object or sequence list.
:param phyche_index: physicochemical properties list.
:param all_property: bool, choose all physicochemical properties or not.
:param extra_phyche_index: dict, the key is the dinucleotide (string), and its corresponding value is a list.
It means user-defined phyche_index.
#################################################################
"""
if 'k' in kwargs:
k = kwargs['k']
else:
k = 3
if 'lag' in kwargs:
lag = kwargs['lag']
else:
lag = 2
if 'phyche_index' in kwargs:
phyche_index = kwargs['phyche_index']
else:
phyche_index = None
if 'all_property' in kwargs:
all_property = kwargs['all_property']
else:
all_property = False
if 'extra_phyche_index' in kwargs:
extra_phyche_index = kwargs['extra_phyche_index']
else:
extra_phyche_index = None
input_data = [input_data]
sequence_list, phyche_value = ReadyAcc(input_data, k, phyche_index, all_property, extra_phyche_index)
from PyDNAacutil import MakeACVector, MakeCCVector
zipped = list(zip(MakeACVector(sequence_list, lag, phyche_value, k),
MakeCCVector(sequence_list, lag, phyche_value, k)))
vec = [reduce(lambda x, y: x + y, e) for e in zipped]
dict_keys = ['TCC_%s'%i for i in range(1,len(vec[0])+1)]
res = dict(zip(dict_keys,vec[0]))
return res
if __name__ == '__main__':
extra_phyche_value = {'AA': [0.06, 0.5, 0.27, 1.59, 0.11, -0.11],
'AC': [1.50, 0.50, 0.80, 0.13, 1.29, 1.04],
'AG': [0.78, 0.36, 0.09, 0.68, -0.24, -0.62],
'AT': [1.07, 0.22, 0.62, -1.02, 2.51, 1.17],
'CA': [-1.38, -1.36, -0.27, -0.86, -0.62, -1.25],
'CC': [0.06, 1.08, 0.09, 0.56, -0.82, 0.24],
'CG': [-1.66, -1.22, -0.44, -0.82, -0.29, -1.39],
'CT': [0.78, 0.36, 0.09, 0.68, -0.24, -0.62],
'GA': [-0.08, 0.5, 0.27, 0.13, -0.39, 0.71],
'GC': [-0.08, 0.22, 1.33, -0.35, 0.65, 1.59],
'GG': [0.06, 1.08, 0.09, 0.56, -0.82, 0.24],
'GT': [1.50, 0.50, 0.80, 0.13, 1.29, 1.04],
'TA': [-1.23, -2.37, -0.44, -2.24, -1.51, -1.39],
'TC': [-0.08, 0.5, 0.27, 0.13, -0.39, 0.71],
'TG': [-1.38, -1.36, -0.27, -0.86, -0.62, -1.25],
'TT': [0.06, 0.5, 0.27, 1.59, 0.11, -0.11]}
phyche_index = \
[[2.26, 3.03, 2.03, 3.83, 1.78, 1.65, 2.00, 2.03, 1.93, 2.61, 1.65, 3.03, 1.20, 1.93, 1.78, 2.26],
[7.65, 8.93, 7.08, 9.07, 6.38, 8.04, 6.23, 7.08, 8.56, 9.53, 8.04, 8.93, 6.23, 8.56, 6.38, 7.65]]
from PyDNAutil import NormalizeIndex
dac = GetDAC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Twist', 'Tilt'])
print(dac)
print(len(dac))
dac = GetDAC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', all_property=True)
print(dac)
print(len(dac))
dac = GetDAC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Twist', 'Tilt'],
extra_phyche_index=NormalizeIndex(phyche_index, is_convert_dict=True))
print(dac)
print(len(dac))
print('\n')
dcc = GetDCC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Twist', 'Tilt'])
print(dcc)
print(len(dcc))
dcc = GetDCC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', all_property=True)
print(dcc)
print(len(dcc))
dcc = GetDCC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Twist', 'Tilt'],
extra_phyche_index=NormalizeIndex(phyche_index, is_convert_dict=True))
print(dcc)
print(len(dcc))
print('\n')
print('DACC')
dacc = GetDACC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Twist', 'Tilt'])
print(dacc)
print(len(dacc))
dacc = GetDACC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC',all_property=True)
print(dacc)
print(len(dacc))
dac = GetDACC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Twist', 'Tilt'],
extra_phyche_index=NormalizeIndex(phyche_index, is_convert_dict=True))
print(dac)
print(len(dac))
print('\n')
phyche_index = [
[7.176, 6.272, 4.736, 7.237, 3.810, 4.156, 4.156, 6.033, 3.410, 3.524, 4.445, 6.033, 1.613, 5.087, 2.169, 7.237,
3.581, 3.239, 1.668, 2.169, 6.813, 3.868, 5.440, 4.445, 3.810, 4.678, 5.440, 4.156, 2.673, 3.353, 1.668, 4.736,
4.214, 3.925, 3.353, 5.087, 2.842, 2.448, 4.678, 3.524, 3.581, 2.448, 3.868, 4.156, 3.467, 3.925, 3.239, 6.272,
2.955, 3.467, 2.673, 1.613, 1.447, 3.581, 3.810, 3.410, 1.447, 2.842, 6.813, 3.810, 2.955, 4.214, 3.581, 7.176]
]
print('Begin TAC')
tac = GetTAC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Dnase I', 'Nucleosome'])
print(tac)
print(len(tac))
tac = GetTAC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC',all_property=True)
print(tac)
print(len(tac))
tac = GetTAC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Dnase I', 'Nucleosome'],
extra_phyche_index=NormalizeIndex(phyche_index, is_convert_dict=True))
print(tac)
print(len(tac))
print('\n')
print('Begin TCC')
tcc = GetTCC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Dnase I', 'Nucleosome'])
print(tcc)
print(len(tcc))
tcc = GetTCC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', all_property=True)
print(tcc)
print(len(tcc))
tcc = GetTCC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Dnase I', 'Nucleosome'],
extra_phyche_index=NormalizeIndex(phyche_index, is_convert_dict=True))
print(tcc)
print(len(tcc))
print('\n')
print('Begin TACC')
tacc = GetTACC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Dnase I', 'Nucleosome'])
print(tacc)
print(len(tacc))
tacc = GetTACC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', all_property=True)
print(tacc)
print(len(tacc))
tacc = GetTACC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC', phyche_index=['Dnase I', 'Nucleosome'],
extra_phyche_index=NormalizeIndex(phyche_index, is_convert_dict=True))
print(tacc)
print(len(tacc))
print('\n')
