python基础知识复习

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>>> bin(5) #二进制 0-1
'0b101'
>>> oct(9) #八进制 0-7
'0o11'
>>> hex(23) #十六进制 0-9 a-f(A-F)
'0x17'

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>>> from fractions import Fraction
>>> x = Fraction(2,5)
>>> y = Fraction(3,7)
>>> x+y
Fraction(29, 35)
>>> x/y
Fraction(14, 15)
>>> x**2
Fraction(4, 25)
>>> y.numerator #分子
3
>>> y.denominator #分母
7

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>>> x = 2.3
>>> x.as_integer_ratio()
(2589569785738035, 1125899906842624)

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import cmath

z = 1 + 2j
sin_z = cmath.sin(z)
print(f"The sin of {z} is {sin_z}")

#极坐标转换表示
r,theta = cmath.polar(z)
print (f"The polar coordinates of {z} are (r={r}, theta={theta})")
print (f"The polar coordinates of {z} are ({r:.2f},{theta:.2f})")

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The sin of (1+2j) is (3.165778513216168+1.959601041421606j)
The polar coordinates of (1+2j) are (r=2.23606797749979, theta=1.1071487177940904)
The polar coordinates of (1+2j) are (2.24,1.11)

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from math import factorial
factorial(70)

import math
math.factorial(70)

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a_list = [1,2,3,4,5]
alist = list(range(1,6))
blst = [1, 'a', 3.6, 2+5j]

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>>> alist + blst
[1, 2, 3, 4, 5, 1, 'a', 3.6, (2+5j)]
>>> blst * 3
[1, 'a', 3.6, (2+5j), 1, 'a', 3.6, (2+5j), 1, 'a', 3.6, (2+5j)]

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alst = [1,2,3,4,5]

#入栈
alst.append(6)

#出栈
alst.pop(-1)

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alst = [1,2,3,4,5]

#入队
alst.append(6)

#出队
alst.pop(0) #移除第一个元素，相当于队列开头元素

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from collections import deque

# 创建一个空队列
queue = deque()

# 入队操作
queue.append('a')
queue.append('b')
queue.append('c')

print(queue)  # 输出：deque(['a', 'b', 'c'])

# 出队操作
item = queue.popleft()
print(item)  # 输出：'a'
print(queue)  # 输出：deque(['b', 'c'])

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a = {}; a = dict() #定义空字典
b = {'x':3, 'y':4}
c = dict(uid=105, login='Lumberjack', name='Michael Palin')

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#输入
read(size)
readline(size)
readlines()

for eachline in file:
    print (eachline)


#输出,写入文件
write(astr)
writelines(str_list)

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A_num = C_num = G_num = T_num = 0

for i in range(len(DNAstr)):
    if DNAstr[i]=='A':
        A_num = A_num + 1
    elif DNAstr[i]=='C':
        C_num = C_num + 1
    elif DNAstr[i]=='G':
        G_num += 1 #another way
    elif DNAstr[i]=='T':
        T_num += 1 #another way
  
print("A_num =", A_num)
print("C_num =", C_num)
print("G_num =", G_num)
print("T_num =", T_num)

total_num = len(DNAstr)
print("A_frq =", A_num/total_num)
print("C_frq =", C_num/total_num)
print("G_frq =", G_num/total_num)
print("T_frq =", T_num/total_num)

dna_dic = {'A': 0, 'C': 0, 'G': 0, 'T': 0} #the dict for DNA numbers
for n in DNAstr:
    dna_dic[n] += 1
print(dna_dic) #print out the DNA numbers in a dict format

dna_frq_dic = {}
DNAs = 'ACGT' #the 4 kinds of nucleiotides
for d in DNAs: #calculate the frequencies
    dna_frq_dic[d] = dna_dic[d]/total_num
print(dna_frq_dic) #print out the DNA frequencies in a dict format

output_file_name = 'D:/frq.txt'
output_file = open(output_file_name, 'wt') #open file in a writing and text model
output_string = '\t'.join(DNAs)
output_file.write(output_string + '\n')
output_string = ''
for d in DNAs:
    output_string += str(dna_dic[d]) + '\t'
output_string = output_string.strip()
output_string += '\n'
output_file.write(output_string)
olst = [] #create a list for DNA frequencies
for d in DNAs:
    olst.append(str(dna_frq_dic[d]))
output_string = '\t'.join(olst) + '\n'
output_file.write(output_string)
output_file.close() #please check the file D:\frq.txt to see what you got

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#This is a demo script for "with" and "file" context manager.

with open('DNAseq.txt','rt') as ifl:
    DNAstr = ifl.read()

DNAlen = len(DNAstr) - 1

A_frq = DNAstr.count('A')/DNAlen
C_frq = DNAstr.count('C')/DNAlen
G_frq = DNAstr.count('G')/DNAlen
T_frq = DNAstr.count('T')/DNAlen

print('A_frq =', A_frq)
print('C_frq =', C_frq)
print('G_frq =', G_frq)
print('T_frq =', T_frq)

with open('DNAfrq.txt', 'wt') as ofl:
    ofl.write('\t'.join(['A', 'C', 'G', 'T'])+'\n')
    #using f-string to format output
    ofl.write(f'{A_frq: .3f}\t{C_frq: .3f}\t{G_frq: .3f}\t{T_frq: .3f}\n'

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def readIntoList(filename):
    ifl=open(filename,'rt')
    iflst=ifl.readlines()
    ifl.close()   
    iflstlen=len(iflst)
    seqlist=[]
    aseq = []
    titstr = ''
    seqstr=''
    for i in iflst:
        i = i.strip()
        if i[0]=='>':
            titstr = i
            if seqstr!='':
                aseq.append(pretitstr)
                aseq.append(seqstr)
                seqlist.append(aseq)    
                seqstr = ''
                aseq = []
        else:
            seqstr += i
            pretitstr = titstr
    aseq = [titstr, seqstr] 
    seqlist.append(aseq)
    return seqlist  
   
faflname = 'Seqs.fasta'

seqlst = readIntoList(faflname)
for s in seqlst:
    print(s[0][:15], s[1][:15])

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def get_sum(a, b=2, *theRestTuple, **theRestDict): 
	print('Sum is', a+b+sum(theRestTuple)+sum(theRestDict.values()) )
调用：get_sum(1,2,3,4,c=5,d=6)

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#变长参数组（元组或字典）：
#非关键字参数（元组）：
def get_sum(a, b=2, *theRest):
	print('The sum is ', a + b + sum(theRest) )
#调用：>>> get_sum(1,2,3,4)
#关键字参数（字典）：
def get_sum(a, b=2, **theRest):
	print('The sum is ', a+b+sum(theRest.values()) )
调用：get_sum(1,2,c=3,d=4)

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class Dog:
    def __init__(self):
        self.mouth = "big"
    def bark(self):
        print("Woof!")

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>>> print(Dog.mouth) 
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: type object 'Dog' has no attribute 'mouth'
>>> print(wangcai.mouth) 
big
>>> print(Dog.bark)  
<function Dog.bark at 0x000002644983EE60>
>>> print(wangcai.bark) 
<bound method Dog.bark of <__main__.Dog object at 0x000002644981B130>>

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class Dog:
    jaw = ["sharp", 32]
    paw = ["cute", 4]
    def __init__(self):
        self.mouth = "big"
  
print(Dog.jaw)
xiaobai = Dog()
print(xiaobai.paw)

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class example:
    def foo():
        print("This is a static method.")  
    foo = staticmethod(foo)

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class example:
    @staticmethod
    def foo():
        print("This is a static method."）

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class Dog:
    head = 1
    tail = 3
  
    @classmethod
    def show_head(cls):
            print('The head is ', cls.head)
    #show_head = classmethod(show_head)
  
    @staticmethod
    def show_tail():
            print('The tail is', Dog.tail)
    #show_tail = staticmethod(show_tail)
  
    def __init__(self):
        self.jaw = 'strong'
  
    def show_jaw(self):
        print('The jaw is', self.jaw)

    def show_head_2(self): 
        print('The head is', Dog.head) 
  
    @classmethod 
    def show_jaw_2(cls):
        print('The jaw is', self.jaw) 

    @staticmethod 
    def show_jaw_3():
        print('The jaw is', self.jaw)


Dog.show_head() 
Dog.show_tail() 
Dog.show_jaw()  
Dog.show_jaw_2()
Dog.show_jaw_3()

adog = Dog() 
adog.show_head() 
adog.show_head_2() 
adog.show_tail() 
adog.show_jaw() 

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class Parent:
    def __init__(self, name):
        self.name = name

    def say_hello(self):
        print(f"Hello, I'm {self.name}")

class Child(Parent):
    def say_goodbye(self):
        print(f"Goodbye, I'm {self.name}")

# 创建一个Child对象
child = Child("Tom")

# 调用从Parent类继承的say_hello方法
child.say_hello()

# 调用Child类自己的say_goodbye方法
child.say_goodbye()

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#
class Molecule:
    def __init__(self):
        self.elements = set()
        self.weight = None

    def show_weight(self):
        print(self.weight)

    def show_elements(self):
        print(self.elements)


class AminoAcid(Molecule):
    def __init__(self):
        super().__init__()
        self.composition = {'C': 0, 'H': 0, 'O': 0, 'N': 0, 'S': 0}

    def calc_mw(self):
        self.weight = self.composition['C']*12.01 + self.composition['H']*1.008 + self.composition['O']*16.00 + self.composition['N']*14.01 + self.composition['S']*32.07

    def show_weight(self):
        self.calc_mw()
        super().show_weight()

    def show_elements(self):
        self.elements = {k for k, v in self.composition.items() if v != 0}
        super().show_elements()
    
class Leucine(AminoAcid):
    def __init__(self):
        super().__init__()
        self.composition = {'C': 6, 'H': 13, 'O': 1, 'N': 1, 'S': 0}

    def show_composition(self):
        print(self.composition)

    def is_isoform(self, other):
        return self.composition == other.composition


class Isoleucine(AminoAcid):
    def __init__(self):
        super().__init__()
        self.composition = {'C': 6, 'H': 13, 'O': 1, 'N': 1, 'S': 0}

    def show_composition(self):
        print("Isoleucine composition: ", self.composition)


class Cysteine(AminoAcid):
    def __init__(self):
        super().__init__()
        self.composition = {'C': 3, 'H': 7, 'O': 2, 'N': 1, 'S': 1}

    def show_composition(self):
        print("Cysteine composition: ", self.composition)


leu = Leucine()
iso = Isoleucine()
cys = Cysteine()

print("Leucine weight: ")
leu.show_weight()
print("Leucine elements: ")
leu.show_elements()
print("Leucine composition: ")
leu.show_composition()
print("Is Isoleucine an isoform of Leucine? ", leu.is_isoform(iso))
print("Is Cysteine an isoform of Leucine? ", leu.is_isoform(cys))

print("Isoleucine weight: ")
iso.show_weight()
print("Isoleucine elements: ")
iso.show_elements()
print("Isoleucine composition: ")
iso.show_composition()

print("Cysteine weight: ")
cys.show_weight()
print("Cysteine elements: ")
cys.show_elements()
print("Cysteine composition: ")
cys.show_composition()

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>>> exec("print({}.fromkeys(range(2)))") #输出{0: None, 1: None}
>>> exec("f = lambda x: x**2"); f(3)
9
>>> exec("def func(x): return x**2"); func(3)
9
>>> astr = "print(x**y)"
>>> a_scope = {'x': 3, 'y': 4}
>>> exec(astr, a_scope)
81

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>>> from math import sin
>>> funstr = ''
>>> for i in range(1,100):
funstr += 'sin(' + str(i) + '*x)' + '+'
>>> funstr = funstr.rstrip('+')
>>> f_val_lst = map(lambda x: eval(funstr), range(100))
>>> sum(f_val_lst)
126.6596615979565

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>>> from math import sin
>>> funlst = [] #函数列表
>>> for i in range(1,100):
exec('def sin_'+str(i)+'(x): return sin('+str(i)+'*x)') #定义函数
funlst.append(eval('sin_'+str(i))) #把函数名添加为列表元素
>>> dir() #查看名字空间，看是否存在sin_i形式的函数名
>>> funlst[0] #查看函数列表的第一个元素，看是否是sin_1
<function sin_1 at 0x000000000339BCF8>
>>> f_val_lst = [sum(map(lambda y: y(i), funlst)) for i in range(100)]
>>> sum(f_val_lst)
126.6596615979565

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>>> eval_code = compile( '3+4', '', 'eval') #可求值表达式
>>> eval_code
<code object <module> at 0000000002C59630, file "", line 1>
>>> eval(eval_code)
7
>>> callable(eval_code) #code对象可执行，但不可调用
False
>>> single_code = compile("print('hello world!')",'','single')
>>> exec(single_code)
hello world!

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>>> exec_code = compile('', '', 'exec')
#三引号（'''或"""）定义多行字符
>>> exec_code = compile('''n = 
input('Count how many numbers?')
for i in range(int(n)):
print(i)
''', '', 'exec')
>>> exec(exec_code)
Count how many numbers?5
0
1
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4

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try:
    x = 1 / 0  # 这将引发一个ZeroDivisionError
except ZeroDivisionError:
    print("You can't divide by zero!")

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class MyException(Exception):
    pass

try:
    raise MyException("This is a custom exception")
except MyException as e:
    print(e)

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#You may copy this line into the console.
ProSeq = 'MNAPERQPQPDGBBGDAPGHEPGGSPQDELDFSILFDYEYLNPNEEEPNAHKVASPPSOOGPAYPDDVLDYGLKPYSPLASLSGEPPGRFGEPDBRVGPQKFLSAAKPAGASGLSPRIEITPSHELIQAVGPLRMRDAGLLVEQPPLAGVAASPRFTLPVPGFEGYREPLCLSPAXSSGSSASFISDTFSPYTSPCVSPNNGGPUDDLCPQFQNIPAHYSPRTSPIMSPRTSLAEDSCLGRHSPVPRPASRSSSPGAXXXKRRHSCAEALVALPPGASPQRSRSPSPQPSSHVAPQDHGSPAGYPPVAGSAVIMDALNSLATDXSPCGIPPKMWKTXSP'

#The 20 normal amino acids
AA20 = 'ACDEFGHIKLMNPQRSTVWY'

#### The dict for amino acid numbers ####
aa_dic = {}
for a in AA20:
    aa_dic[a] = 0

#### The try-except clauses ####
for a in ProSeq:
    try:
        aa_dic[a] += 1
    except KeyError: # or # except:
        print('Find an abnormal amino acid:', a)


print(aa_dic)

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# 使用map和lambda函数来对列表中的每个元素加1
nums = [1, 2, 3, 4, 5]
nums_plus_one = map(lambda x: x + 1, nums)
print(list(nums_plus_one))  # 输出 [2, 3, 4, 5, 6]

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class TestIterator:
	value = 0
	def __next__(self):
		self.value += 1
		if self.value > 10: 
			raise StopIteration
			return self.value
	def __iter__(self):
		return self
ti = TestIterator()
list(ti)#[1, 2, 3, 4, 5, 6, 7, 8, 9, 10]

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>>> a = eval("(abs(x) for x in [-1,2,-3,4])")  
>>> a.__next__()
1
>>> a.__next__()
2

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>>> nested = [[1,2], [3,4], [5]]
>>> def flatten(nested):
	for sublist in nested:
		for element in sublist:
			yield element
			#print(element)
>>> for num in flatten(nested): #逐行输出各个数字
	print(num)
>>> list(flatten(nested)) #返回数字列表 [1, 2, 3, 4, 5]

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>>> import sys
>>> print(sys.path)
['', 'E:\\coding\\Miniforge3\\envs\\dzx\\python310.zip', 'E:\\coding\\Miniforge3\\envs\\dzx\\DLLs', 'E:\\coding\\Miniforge3\\envs\\dzx\\lib', 'E:\\coding\\Miniforge3\\envs\\dzx', 'E:\\coding\\Miniforge3\\envs\\dzx\\lib\\site-packages', 'E:\\coding\\Miniforge3\\envs\\dzx\\lib\\site-packages\\win32', 'E:\\coding\\Miniforge3\\envs\\dzx\\lib\\site-packages\\win32\\lib', 'E:\\coding\\Miniforge3\\envs\\dzx\\lib\\site-packages\\Pythonwin']

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#从Biopython中引入序列类
from Bio.Seq import Seq

#生成一个含有A、C、G、T的字符串
astr = 'ATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGA'

#生成一条DNA序列，即，Seq类的一个实例
dna_seq = Seq(astr)

#查看序列对象
dna_seq
print(dna_seq)

#查看DNA序列的第一个字符、最后一个字符、前10个字符
dna_seq[0]
dna_seq[-1]
print(dna_seq[:10])

#把DNA序列当成普通字符串，用循环依次输出其字符
for a in dna_seq:
    print(a)

#查看DNA序列对象的属性和方法
dir(dna_seq)

#计算DNA序列中G的含量
G_num = dna_seq.count('G')
print('G content is :', G_num/len(dna_seq))

  
#得到DNA序列的互补序列
c_dna_seq = dna_seq.complement()
c_dna_seq

#得到DNA序列的反向互补序列
rc_dna_seq = dna_seq.reverse_complement()
rc_dna_seq

#调用转录方法，得到RNA序列
rna_seq = dna_seq.transcribe()
rna_seq

#调用翻译方法，得到Protein序列
pro_seq = dna_seq.translate()
pro_seq

#计算蛋白序列中氨基酸T出现的次数
pro_seq.count('T')

#查看蛋白序列对象的属性和方法
dir(pro_seq)

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from Bio.PDB import *
#查看当前环境中定义了哪些变量、函数和类
dir()

pdbflname = 'pdb4xb7.ent'

#调用PDBParser()类，创建一个PDBParser对象，解析PDB文件
parser = PDBParser()
struct = parser.get_structure('s1', pdbflname)

for model in struct.get_iterator():
   for chain in model.get_iterator():
       for chain in model.get_iterator():
           for residue in chain.get_iterator():
               for atom in residue.get_iterator():
                   print(atom)
       
atomcord = [0, 0, 0]; atomnum = 0

for model in struct.get_iterator():
   for chain in model.get_iterator():
       for chain in model.get_iterator():
           for residue in chain.get_iterator():
               for atom in residue.get_iterator():
                    atomcord[0] += atom.get_coord()[0]
                    atomcord[1] += atom.get_coord()[1]
                    atomcord[2] += atom.get_coord()[2] 
                    atomnum += 1
                       
geomcenter = (atomcord[0]/atomnum, atomcord[1]/atomnum, atomcord[2]/atomnum)

print('geometric center is:', geomcenter)