清单和清单问题清单

Question

我正在写一个程序。我的蟒蛇经验有限。该程序采用csv文件来创建列表。txt文件接受一串字符，并将其转换为into列表。然后，我必须将列表与列表中的in进行比较。这是比较DNA的匹配。这个程序只适用于一个问题。我的csv文件中有三个不同的DNA字符串要比较，另一个文件有8条，我可以让它们一起工作，但是它需要对行进行调整，以创建列表、chdnalist和子序列。当前使用[[]、[]、[]]运行，它将只运行带有3个字符串的较小的列表。我可以总共添加8 []，但是当然，它不能处理3字符串的集合。

下面是我的代码副本：

import csv
import sys

def main():

    # TODO: Check for command-line usage
    if len(sys.argv) != 3:
        print("Missing Files!")
        sys.exit(1)
    # TODO: Read database file into a variable
    dnalist = []
    with open(sys.argv[1], "r", newline = '') as subject_file:
        dnalst = csv.reader(subject_file)
        for row_list in dnalst:
            dnalist.append(row_list)

    # TODO: Read DNA sequence file into a variable
    with open(sys.argv[2], "r") as f:
        sequence = f.read()

    # TODO: Find longest match of each STR in DNA sequence
    chdnalist = [[],[],[]]
    subsequence = [[],[],[]]
    for q in range(1, len(dnalist[0])):
        subsequence[q - 1] = dnalist[0][q]
    for t in range (len(subsequence)):
        chdnalist[t] = longest_match(sequence, subsequence[t])


    # TODO: Check database for matching profiles
    compare(dnalist, chdnalist)
    return

def longest_match(sequence, subsequence):
    """Returns length of longest run of subsequence in sequence."""

    # Initialize variables
    longest_run = 0
    subsequence_length = len(subsequence)
    sequence_length = len(sequence)


    # Check each character in sequence for most consecutive runs of subsequence
    for i in range(sequence_length - 1):

        # Initialize count of consecutive runs
        count = 0

        # Check for a subsequence match in a "substring" (a subset of characters) within sequence
        # If a match, move substring to next potential match in sequence
        # Continue moving substring and checking for matches until out of consecutive matches
        while True:

            # Adjust substring start and end
            start = i + count * subsequence_length
            end = start + subsequence_length

            # If there is a match in the substring
            if sequence[start:end] == subsequence:
                count += 1

            # If there is no match in the substring
            else:
                break

        # Update most consecutive matches found
        longest_run = max(longest_run, count)

    # After checking for runs at each character in seqeuence, return longest run found
    return longest_run

def compare(dnalist, chdnalist):
    for name, *dna in dnalist[1:]:
        dna = list(map(int, dna))
        if dna == chdnalist:
            print(name)
            return
    print("No match")

main()

下面是一个小型csv文件的副本：

name,AGATC,AATG,TATC
Alice,2,8,3
Bob,4,1,5
Charlie,3,2,5

下面是一个大型csv文件的副本：

name,AGATC,TTTTTTCT,AATG,TCTAG,GATA,TATC,GAAA,TCTG
Albus,15,49,38,5,14,44,14,12
Cedric,31,21,41,28,30,9,36,44
Draco,9,13,8,26,15,25,41,39
Fred,37,40,10,6,5,10,28,8
Ginny,37,47,10,23,5,48,28,23
Hagrid,25,38,45,49,39,18,42,30
Harry,46,49,48,29,15,5,28,40
Hermione,43,31,18,25,26,47,31,36
James,46,41,38,29,15,5,48,22
Kingsley,7,11,18,33,39,31,23,14
Lavender,22,33,43,12,26,18,47,41
Lily,42,47,48,18,35,46,48,50
Lucius,9,13,33,26,45,11,36,39
Luna,18,23,35,13,11,19,14,24
Minerva,17,49,18,7,6,18,17,30
Neville,14,44,28,27,19,7,25,20
Petunia,29,29,40,31,45,20,40,35
Remus,6,18,5,42,39,28,44,22
Ron,37,47,13,25,17,6,13,35
Severus,29,27,32,41,6,27,8,34
Sirius,31,11,28,26,35,19,33,6
Vernon,26,45,34,50,44,30,32,28
Zacharias,29,50,18,23,38,24,22,9

这里是一个文本文件的副本，当我在一个小csv文件中运行时，程序将返回一个匹配给Bob。

AAGGTAAGTTTAGAATATAAAAGGTGAGTTAAATAGAATAGGTTAAAATTAAAGGAGATCAGATCAGATCAGATCTATCTATCTATCTATCTATCAGAAAAGAGTAAATAGTTAAAGAGTAAGATATTGAATTAATGGAAAATATTGTTGGGGAAAGGAGGGATAGAAGG

此文件将从大型csv文件返回与露娜的匹配：

/*
* 提示：该行代码过长，系统自动注释不进行高亮。一键复制会移除系统注释 
* TCTATTCTTTGAGGATACGCTCGGCCTAGGCGGGGCTAATGGAAGCCAGGCTAATCCGATGTTGCGGTGCACCTCGATACCGTTCTAAAATATCACATCAACGCGCTCCAGTTGTGTGCCAAGGCCCGCTGAAGAGCAATGGAGCACCTACCCGGCCTTCTAACGCTGTCTAAAACTCCAAGCGAATTGCAGATTTTGGTTAGGACCCGTTTAATCTGTGGGCTTTGGTACTATGCAACCAATGGAACCGGTCGGACTCTGATCAGTCCCGACTGACAGGTCTCAAGTAGTTTGCTTACACGTTCTGACCCCCGTGCGCACCGTTGGGCGTACAGCGGTTCGGTCTATGGAATCAAGGAAAATCATTCGTATGGGGACGTAGTCACATAACAGCTGCAGGGAACTATGGAGATGACGAGGGGTCGTTTAGTGGAACGTCAAATGTCCTAACTGGTTCTGAGCTGTCTGGAACGTTGCAGTCAACGTCTACGATCTGGATTCTACAGTCTAGGCGTTCCAAGGGGCACCAGTAAGCTAAGTTGTTTAAATATGGCGGGTGTCGAAATGACGTCCAAAATCGCAAATAAGACAGATAGCAGGGGTGCAACTTAGGTATCTAAGGTAACTCTGACATACCTCATACAACTATCGAACAGTGGATTCCTTGTCGTCCTGTTGTAAACAGTTCAAGTCGGTACATGTTAGCGGGTGGTTTGGACGAGTATACAGGACCTGGCCTACACGGAATGTTTTAGATTCTATGTCCGGCGGGGACATCGCGTGCCGCTAGGATATAATTGGATTGTGGGAAGAATTTGGCCGGATTTTTGGCCTAGACTCGCGCTTCAGACCATACCGTGCGATCAGCACGATTGCTGACAAGCGTCGGTATTAAAGCAGGCTCCTTCCCAGCCAAACTAACCCAACGAAGACATCATGTTTCGCCGAAGTATCTTTGGGAGATGGGCGAATTAATCGCTTAGCGTGGCCGACTTGGGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGTTTAAGGGACTTATCCGACCAGAGGGGCAGTTACTTGTGGCGGTCACACGCCAGGACGAGTCTGTTCTTGCTGTGCGTAGATTAGGCTTGATCTGTGACTACAGGCGAATAGTAGGTGTGGGAAACAGAGGGGGGAGCAATGTGATCCCGGGGGGAGTGCTTCCTATACCTCGGTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGAATGGATTATCCCCACCCAATGATCCGATCGCAAGCCTTAATACCATGGCACACCTCTCAACCTACTGATCTTCCATCCGTTTAACCCAGCACTAAGCTGCTCAGTGGTCACACTATGTTCAAGCTTCCGTGACGTGGGATCCTGGGGTCTTCGCAAGGCTAGTTTTGACCATTATCGACGACCGTCACCCTGTGACTGGTTCCCAACAAGGTGTCAAGTTCTAGCCCGTACCTGCAATCGGGAACCTCCGGTGCTTCATGAACCATGGATATAGGAATTATTGGTCTCCTCTCGCGTAGGTAGCGCGAATACCCCCAAGATGACACACTGTGGTGAACTTTGAGGACTCCCAGAAGGGTGACGGGTTATGTGGTTACGCGAAGTCGGCGTATCCACCGCCTAATTTTAAATTCAGCTCGAGCGACACGCGCGCTTCCTGGAAACGTTAGACGGGAAAAACCCCGCCCGAGAATGCGGGTTCCGCGGCCCACTAGGGGGCCCCCCAAGGATCTGACCGCGTATAAGCAATGCACAGCTGTACCATTTCAAATAGGACAGATAGTACCCCCACCGTGACTCGGCCTCAGATAATGGAATACGACCTGGTGACGGCGGTAGGGGTTCTATCTCAGGTATTCAGAGGGTGCATCCAGGTGATTCGTCACGTCCCGATTTCGACCCCACCACAGGATTTGTGCGATGGTAGTCTTGATGCTGTTTGCAGGCGGCCAAGCATCTAGGAGATGCCTCACTGCGCGAGATGAACCGGCGTTTCACAAGGGGACGCCAGGCCTTGCCGTCTCCATAAACCACGAGAAGGTATCGAACGTCAAACGGATAAATGCCGCGATACCGCTCGTTTCGAAGCGGCACTTCGATGGAAATGAGTAGTATGGCCTCGCCACACGACTACTCATCGGCTTGCGCTGACATCAATCCTGGCTGGCTTGAGGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGCTCCATAGGAAGGTGCGGGATAGCGGACAGCTAATCGGACAGAAGGGCCAGCTTGCACTCTCCTATAATTAGCAAGCGCCATACAATTGTAATCACGTATAAAATACAGCTACGTAAGTAATAGAGAGGCTCCCGGACTGTCCGGCGTCCCGCCAGTCTCGTACCAGGAGGTGGGATGGTAGGCAAACGAGCCTACTAGAATTGGGCCACCCTGTGAATAATATGCAGAGGCAACTACAGACGTCCGTCACCTGCCTAGAATCGAGTTCATTGACGGTGGGATATGCTCCGTTACCTGACTGTAGTTCGACTTTGTGGTGCGCACATAACGAGTGTCTACGATGCACAAAGTGTGAGCAAATTAGGAGTGTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTGCCGAGATGTTGGCGGGAAGTGTACGGCTTTGCGTCGTCGAGTGCTACGCAGTGTGCTACACTCCCGCAGCTGAGGCTAGGGCCCGAAACTAGACATTTTTTCTTTTGGCACTTCGTTCCGTATAATGAGTTCCCTCAATTCCCCGTCCGCAAGCCTCAGGATTACAATTAATTATACGGTTAAAGTTGGCTGCCAAGCCCGTTATTGACCGGTACCTGAGTCGAGGGGGGGTTGGGGATAGGCAATTATAGTATTCACTCACAGGACGCTCAGTAATGCCGCCGTTGTACTTCACGTAAGGGCCACAGTTTTTCTACCACAGAGGATGATCTGAGGACAGCGGTGCGTGAAGCCCGCTATTCAGGACACCCTCGAAACCCGTGGTTCACAGACAAAAAATTCGCCGCGGAAGCTGTTGCCCCTATGCCCCGGGTCAGCAAGGAGTCTGGATTTTATTCCAAGACTGCGTCTTTATTTTCTGGTGAGTATGAAATGACTCTGAGAAAATGGTCGAACCACGAGCTAGCTACAGCCACAGTCCGCTCAACTAACTTACCTCTACTCTAACAGTTACACGGCTTCCCGTTTTATGGGAAGAAGCACCTGTTCCTTTCCCAAGCCCCTTATAGCAGAGGTTGGTATTCGGTTGATTTGGAATAGTTAAACAGCGGCTATTTTGTAATCACTTTCCAGTCGGTAAGACATTCGAACCTCGTTTTGACGCTGCTCGCCATCGCGTTCGACTAGGAGTATTCCACTTTTCGGAGAGATGATTACTCATGACGCGGGGAACTCCATGGCTGTCATGCAGGATCTGGGCTAAATAAGATTAGATGTTCAACTGTCGTATACTTACTGCTACCAGCGGTGCTAGGCCCAGGACCCGCCATACCTGGCTATTGATCACTCTACCAGATGTCTCTTGACGAGTTACGAATTGCTGGGTGCTCTTGGAGACGAGTTGAGTCCGTAGTCGTGGCTGGGGAACGGGCGAGTTCGTACGTACCGTTTCAAAGCCCCACGAACCCAACCTCTTAGCCTTAACCCCACATTAGATACCCAAGTTGCATGACGCATTATGCGAGTACGACACTGGTATCGGCTGATCCGTCACTGCTCAAAGTCCAGTGGTTTCCTTATCTCGGGCTGGAAAGTGTAGCTTGTTCCAAACCTTCGAGAGGTTGATCGATGACCGGTTCTCACACACATCTTGCGGAGGGATGCTTGCGATGTGGCTTTACGTCCACCGACGGGCCGACTAGCTGGAAATCACAAACCCCTGCTCCGATAAGGTATTCTCGTTGACTTAGGGTAAACAAAATGCCCGTTACGTCCTAACCGAGTTTCCGGGCCTTCACTACCCGCGAGGGATGTGTAGTGGGGCCATTTACCTAAGCAGATGTACACCGAGTTACGATAGTCACATGGCCATTCAAAGCGTCTCACATAATCGATCGATAGATGATGTCTAGTCTAGTCTAGTCTAGTCTAGTCTAGTCTAGTCTAGTCTAGTCTAGTCTAGTCTAGTCTAGAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCAGATCCCGGAGGAAGCTGCGATTGGAATGCGGCTAACTTCGCTCTGCAACATTCTTGGCAGACGGCCCCAATGGCGTAATTTAGGCGTGTGTACCTAAAGTGGTCTACTCCTATGAACCGAATCGCGGGATAAATCGAGTTGGGACTGCTTTGCCTTAATTACATTCACTGATTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGGTCGAGCACGGCTGGCACGTCCGGCTCCATCGCGTCGTAATCCATCCCTATTCGACCAACAAAACCTCAGGGGACGGGATGTGAGTGGGTATCGATCATTATCGAACGCCCATAAGTACTCCACTCATCTGTCTGAAAAGTTTGTCGAGTGCCGCTCTCTGAAGAGTACGATAACTTACTCCAAACACTCTACGCCTAGTGGTCGAAAACACTAAAGGGAAAATACTCACTGACTTACTCTGTCGCTCTACGATTGCCGCGATACCTTAATAAGACACGTATCGGCTGTCGCAGCGATGGATTCCTTAAGCGATACAACTAAGATCAATCGGTGCCGGGCCTACAGCCTGGGCCCTAGCTCCAAAAGTGATAATGGATAGTCGGTTCAAGCGAATTTACACCAGACTGATCCTTTACGGTCATTCCGACCGCCGCATGATACATGCCAAAAGACACTTGTCTTCTTTCCTCTAAAAGACAGACCTTGTTTGCAAGGAGAGCCCAATCGGCACGACCCAAAGGGATTATCAACTGAACTATTATTGCATACTACTAAGCAGACGGACCGTATAGCATCATTGATACCTATTATATTTCCATACACCAACTCCATACGCGATGGGTCGAAACTACAAGCTTCACTTACGTGTACAGCCGCAGGACCCACTCTCTAATCTAGCCAATGACACTACTAATTTGAACATTCCCCAGCGATGAACAGGCACATGAGCGGTCCTCGTACCCACCACGGCCCGCTCAACTGCAAGGGGCCGCTCGGATCAAAGTTTTTCACTAACTCATGTCGAGCAGATCGGCATGCTCAAGATAGTATTTTAGGAGG
*/

Answer 1

没有必要根据索引初始化空列表和迭代，例如清单理解将提供一种更简洁、更少错误的方法来实现相同的结果。

subsequence和chdnalist的构造可以这样固定：

# TODO: Find longest match of each STR in DNA sequence
subsequence = [x for x in dnalist[0][1:]]
chdnalist = [longest_match(sequence, s) for s in subsequence]