以下是一个使用Python解析FASTA文件并计算最大ORF长度的示例代码:
def read_fasta(file_path):
sequences = []
with open(file_path, 'r') as file:
sequence = ''
for line in file:
line = line.strip()
if line.startswith('>'):
if sequence:
sequences.append(sequence)
sequence = ''
else:
sequence += line
if sequence:
sequences.append(sequence)
return sequences
def find_orf(sequence):
orfs = []
start_codon = 'ATG'
stop_codons = ['TAA', 'TAG', 'TGA']
start_indices = [i for i in range(len(sequence)) if sequence[i:i+3] == start_codon]
for start_index in start_indices:
stop_index = None
for i in range(start_index+3, len(sequence)-2, 3):
codon = sequence[i:i+3]
if codon in stop_codons:
stop_index = i + 3
break
if stop_index:
orfs.append(sequence[start_index:stop_index])
return orfs
def get_max_orf_length(sequences):
max_orf_length = 0
for sequence in sequences:
orfs = find_orf(sequence)
for orf in orfs:
orf_length = len(orf)
if orf_length > max_orf_length:
max_orf_length = orf_length
return max_orf_length
fasta_file = 'sequences.fasta'
sequences = read_fasta(fasta_file)
max_orf_length = get_max_orf_length(sequences)
print("Maximum ORF length:", max_orf_length)
要运行此代码,您需要将FASTA文件的路径替换为fasta_file变量的值。这段代码首先定义了三个函数:read_fasta函数用于从FASTA文件中读取序列,find_orf函数用于在一个序列中查找ORF,get_max_orf_length函数用于计算最大ORF长度。最后,代码读取FASTA文件,调用相应函数,并打印出最大ORF长度。
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