Question

所以我的任务是在文本文件中加入文本，但是就像我尝试的任何东西都无法正常工作。我尝试了split，但是它需要字符串而不是数组，而join根本对我没有帮助，因为我已经有可以完成这项工作的代码。

带有文字的文本文件如下（文件名= demo_fasta_file_2019.fsa）：

>sequence_1
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
>sequence_2
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
GATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGAGATCGATCGA
>sequence_3
TTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAA
TTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAATTTTGGAAAA
>sequence_4
GGTTAACCATGGATC

我拥有的代码如下：

#def Read_FastA_Names_And_Sequences(filepath):

#############
filepath=str("demo_fasta_file_2019.fsa")
##sequence_names,sequences = Read_FastA_Names_And_Sequences(filepath)
sequence_names=[]
sequences=[]
number_of_sequences=4
#############
textfile = open(filepath, 'r')

sequence = textfile.readlines()

for i in sequence:
    if i.__contains__('>'):
        a=i[1:]
        sequence_names.append(a[:a.__len__()-1])
    i=+1
print(sequence)
#list1 = sequence
#s = "\n"
#s = s.join(list1)
#print(s)
list2 = sequence
words2 = list2.split(">")
print(words2)

所以我的问题是，我如何只加入不包含> sequence_1，> sequence_2，> sequence_3，> sequence_4的文本？

Answer 1

使用Biopython可以轻松实现，对于在fasta文件上执行其他任务也可能有用：

from Bio import SeqIO

concatenated_sequence = ""

fasta_sequences = SeqIO.parse(open(input_file),'fasta')
for fasta in fasta_sequences:
    # id is stored in fasta.id
    # the sequence is stored in fasta.seq, and need to be transformed to str()
    concatenated_sequence +=  str(fasta.seq)

Answer 2

您可以使用生成器表达式过滤不以>开头的行，并使用str.join对其进行串联：

print(''.join(line for line in open("demo_fasta_file_2019.fsa") if not line.startswith('>')))

如何串联文本文件中的行？

2 个答案: