week 1 practice—— 产生DNA互补链

一、计算某个string中长度为k的情况下，出现比例最高的字符串

# Copy your updated FrequentWords function (along with all required subroutines) below this line

def FrequentWords(Text, k):

    words = []

    freq = FrequencyMap(Text, k)

    m = max(freq.values())

    for key in freq:

        # add each key to words whose corresponding frequency value is equal to m

        if freq[key]==m:

            pattern=key

            words.append(pattern)

    return words

    # your code here

# Copy your FrequencyMap() function here.

def FrequencyMap(Text, k):

    freq = {}

    n = len(Text)

    for i in range(n-k+1):

        Pattern = Text[i:i+k]

        if Pattern in freq:

            freq[Pattern]+=1

        else:

            freq[Pattern]=1

    # hint: your code goes here!

    return freq

# Now set Text equal to the Vibrio cholerae oriC and k equal to 10

Text="ATCAATGATCAACGTAAGCTTCTAAGCATGATCAAGGTGCTCACACAGTTTATCCACAACCTGAGTGGATGACATCAAGATAGGTCGTTGTATCTCCTTCCTCTCGTACTCTCATGACCACGGAAAGATGATCAAGAGAGGATGATTTCTTGGCCATATCGCAATGAATACTTGTGACTTGTGCTTCCAATTGACATCTTCAGCGCCATATTGCGCTGGCCAAGGTGACGGAGCGGGATTACGAAAGCATGATCATGGCTGTTGTTCTGTTTATCTTGTTTTGACTGAGACTTGTTAGGATAGACGGTTTTTCATCACTGACTAGCCAAAGCCTTACTCTGCCTGACATCGACCGTAAATTGATAATGAATTTACATGCTTCCGCGACGATTTACCTCTTGATCATCGATCCGATTGAAGATCTTCAATTGTTAATTCTCTTGCCTCGACTCATAGCCATGATGAGCTCTTGATCATGTTTCCTTAACCCTCTATTTTTTACGGAAGAATGATCAAGCTGCTGCTCTTGATCATCGTTTC"

k=10

# Finally, print the result of calling FrequentWords on Text and k.

print(FrequentWords(Text,k))

二、产生DNA互补链

1.将string形式的DNA链反转

def Reverse(Pattern):

    # your code here

    n=len(Pattern)

    time=0

    rev=""

    for i in range(n):

        rev=Pattern[time]+rev

        time+=1

    return rev

2.互补链

# Input: A DNA string Pattern

# Output: The complementary string of Pattern (with every nucleotide replaced by its complement).

def Complement(Pattern):

    # your code here

    n=len(Pattern)

    com=""

    time=0

    for i in range(n):

        if Pattern[time]=="A":

            com=com+"T"

        elif Pattern[time]=="T":

            com=com+"A"

        elif Pattern[time]=="C":

            com=com+"G"

        else:

            com=com+"C"

        time+=1

    return com

3.根据以上两个程序根据DNA单链生成对应的5‘-3’的互补链

# Output: The reverse complement of Pattern

def ReverseComplement(Pattern): 

    rev=Reverse(Pattern)

    com=Complement(rev)

    return com

# Copy your Reverse() function here.

def Reverse(Pattern):

    # your code here

    n=len(Pattern)

    time=0

    rev=""

    for i in range(n):

        rev=Pattern[time]+rev

        time+=1

    return rev

# Copy your Complement() function here.

def Complement(Pattern):

    # your code here

    n=len(Pattern)

    com=""

    time=0

    for i in range(n):

        if Pattern[time]=="A":

            com=com+"T"

        elif Pattern[time]=="T":

            com=com+"A"

        elif Pattern[time]=="C":

            com=com+"G"

        else:

            com=com+"C"

        time+=1

    return com

三、从基因组中查找计算得出的Pattern的位置

def PatternMatching(Pattern, Genome):

    positions = [] # output variable

    # your code here

    n=len(Genome)

    k=len(Pattern)

    for i in range(n-k+1):

        test=Genome[i:i+k]

        if test==Pattern:

            positions.append(i)

    return positions

四：实际应用——包括读取基因组数据

# Copy your PatternMatching function below this line.

def PatternMatching(Pattern, Genome):

    positions = [] # output variable

    # your code here

    n=len(Genome)

    k=len(Pattern)

    for i in range(n-k+1):

        test=Genome[i:i+k]

        if test==Pattern:

            positions.append(i)

    return positions

# The following lines will automatically read in the Vibrio cholerae genome for you and store it in a variable named v_cholerae

import sys                              # needed to read the genome

input = sys.stdin.read().splitlines()  #

v_cholerae = input[1]                  # store the genome as 'v_cholerae'

# Call PatternMatching with Pattern equal to "CTTGATCAT" and Genome equal to v_cholerae,

# and store the output as a variable called positions

Pattern="CTTGATCAT"

positions=PatternMatching(Pattern,v_cholerae)

# print the positions variable

print (positions)