如何编写Python程序（不使用biopython）来从多fasta文件中读取并列出每个序列的所有开放阅读框（ORF）

Question

我是学习Python的初学者，需要一些帮助来尝试从多fasta文件中获取以下详细信息：

1. 以多 fasta 格式列出每个序列的所有三个阅读框中的所有 ORF
2. 列出编号。每个序列的 ORF 和最长 ORF 及其位置
3. 找出最长 ORf 的以“>”开头的标识符/序列描述。

我似乎连 ORF 的查找都无法正确:')。我真的很感激我能得到的所有帮助。

我尝试列出每个序列中的 ORF，并通过首先制作一个字典来对它们进行计数，字典的键是以“>”开头的序列描述/标识符，值是序列本身。

我的代码：

def findcodon(file,frame):
    f=open(file)
    dictionary=makedictionary(file)
    mlist = list(dictionary.values())
    orfcount=0
    startpos=0
    endpos=0
    stopcodon=['tga','tag','taa','TGA','TAG','TGA']
    startcodon=['ATG','atg']
    for i in mlist:
        for j in range(frame,len(i),3):
            codon=i[j:j+3]
            if codon in startcodon:
                startpos=int(j)
            elif codon in stopcodon:
                endpos=int(j)
        orf=i[j][startpos:endpos]
        orfcount+=1
        print('orf',orfcount,':',orf)
        print('total no.of orfs:',orfcount)


findcodon('myseq.txt',1)

我的输出：

orf 1 : 
total no.of orfs: 1
orf 2 : 
total no.of orfs: 2
orf 3 : 
total no.of orfs: 3
orf 4 : 
total no.of orfs: 4
orf 5 : 
total no.of orfs: 5

Answer 1

def find_codon(file, frame):
    # Open the file and read sequences into a dictionary
    dictionary = {}
    with open(file, 'r') as f:
        identifier = ''
        sequence = ''
        for line in f:
            line = line.strip()
            if line.startswith('>'):
                if identifier:
                    dictionary[identifier] = sequence
                identifier = line
                sequence = ''
            else:
                sequence += line

        # Add the last sequence
        if identifier:
            dictionary[identifier] = sequence

    # Define start and stop codons
    stop_codons = {'tga', 'tag', 'taa'}
    start_codon = 'atg'

    # Iterate through each sequence
    for identifier, sequence in dictionary.items():
        orf_count = 0
        longest_orf = ('', '', 0)  # (ORF, position, length)

        # Loop through each reading frame
        for i in range(frame):
            start_pos = None
            for j in range(i, len(sequence), 3):
                codon = sequence[j:j+3].lower()
                if codon == start_codon:
                    start_pos = j
                elif codon in stop_codons and start_pos is not None:
                    orf_count += 1
                    orf = sequence[start_pos:j+3]
                    orf_length = j - start_pos + 3
                    if orf_length > longest_orf[2]:
                        longest_orf = (orf, start_pos, orf_length)
                    print(f'ORF {orf_count}: {orf} at position {start_pos}')
                    start_pos = None

        print(f'Total number of ORFs: {orf_count}')
        if longest_orf[0]:
            print(f'Longest ORF: {longest_orf[0]} at position {longest_orf[1]}')

# Example usage
find_codon('example_fasta.fasta', 3)