从字典中将解析的fasta文件写回fasta格式

Question

我创建了一个解析Fasta文件的函数，因为我需要删除一些奇怪的字符。现在我有了一本字典，想把它转换成fasta格式。我对Fasta文件并不熟悉，所以我不知道该如何处理。

词典的格式如下：

{'NavAb:/1126': 'TNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQMRKI', 'Shaker:/1656': 'SSQAARVVAIISVFVILLSIVIFCLETLEDEVPDITDPFFLIETLCIIWFTFELTVRFLACPLNFCRDVMNVIDIIAIIPYFITTLNLLRVIRLVRVFRIFKLSRHSKGLQIL', .....

职能：

def parse_file(input_file):
parsed_seqs = {}
curr_seq_id = None
curr_seq = []
for line in newfile:
  line = line.strip()
  line = line.replace('-', '')
  if line.startswith(">"):
     if curr_seq_id is not None:
        parsed_seqs[curr_seq_id] = ''.join(curr_seq)
  curr_seq_id = line[1:]
  curr_seq = []
  continue

curr_seq.append(line)
parsed_seqs[curr_seq_id] = ''.join(curr_seq)
return parsed_seqs

newfile = open("file")
parsed_seqs = parse_file(newfile)
print(parsed_seqs)

Answer 1

如果可以将现有库用于此任务，则可以使用黑云母。

import biotite.sequence.io.fasta as fasta

seq_dict = {
    'NavAb:/1126': 'TNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVAISLVPTSSGFEILRVLRVLRLFRLVTAVPQMRKI',
    'Shaker:/1656': 'SSQAARVVAIISVFVILLSIVIFCLETLEDEVPDITDPFFLIETLCIIWFTFELTVRFLACPLNFCRDVMNVIDIIAIIPYFITTLNLLRVIRLVRVFRIFKLSRHSKGLQIL'
}

fasta_file = fasta.FastaFile()
for header, seq_str in seq_dict.items():
    fasta_file[header] = seq_str
fasta_file.write("path/to/file.fasta")

path/to/file.fasta

>NavAb:/1126
TNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFNQIVITIFTIEIILRIYVHRISFFKDPWSLFDFFVVA
ISLVPTSSGFEILRVLRVLRLFRLVTAVPQMRKI
>Shaker:/1656
SSQAARVVAIISVFVILLSIVIFCLETLEDEVPDITDPFFLIETLCIIWFTFELTVRFLACPLNFCRDVMNVIDIIAIIP
YFITTLNLLRVIRLVRVFRIFKLSRHSKGLQIL

请注意，我属于这个包的开发人员。在许多其他包中也有解决方案，比如Biopython。