使用字符列表在输出中重复写入 - python

Question

在一个文件中，我有一些字符要被替换。

字母 = ["B", "Z", "J", "U", "O"]

for record in SeqIO.parse(inFile, "fasta"):
    for letter in letters:
        if letters in str(record.seq):
            print record.id 
            record.seq = str(record.seq).replace(letter, "X")
            outFile.write(">%s\n%s\n" % (record.description, record.seq))
        else:
            outFile.write(">%s\n%s\n" % (record.description, record.seq))
            #pass

问题是输出看起来像这样，用字母写出尽可能多的字符输出：

> >ID:WP_004160595.1|Erwinia_amylovora_01SFR-BO|01SFR-BO|50S_ribosomal_protei..|630|NZ_CAPA01000010(58437):26053-26682:-1
> MIGLVGKKVGMTRIFTEDGVSIPVTVIEIEANRVTQVKGLENDGYTAIQVTTGAKKANRVTKPAAGHFAKAGVEAGRGLWEFRTAEGAEFTVGQSINVDIFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQLGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA
> >ID:WP_004160595.1|Erwinia_amylovora_01SFR-BO|01SFR-BO|50S_ribosomal_protei..|630|NZ_CAPA01000010(58437):26053-26682:-1
> MIGLVGKKVGMTRIFTEDGVSIPVTVIEIEANRVTQVKGLENDGYTAIQVTTGAKKANRVTKPAAGHFAKAGVEAGRGLWEFRTAEGAEFTVGQSINVDIFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQLGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA
> >ID:WP_004160595.1|Erwinia_amylovora_01SFR-BO|01SFR-BO|50S_ribosomal_protei..|630|NZ_CAPA01000010(58437):26053-26682:-1
> MIGLVGKKVGMTRIFTEDGVSIPVTVIEIEANRVTQVKGLENDGYTAIQVTTGAKKANRVTKPAAGHFAKAGVEAGRGLWEFRTAEGAEFTVGQSINVDIFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQLGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA
> >ID:WP_004160595.1|Erwinia_amylovora_01SFR-BO|01SFR-BO|50S_ribosomal_protei..|630|NZ_CAPA01000010(58437):26053-26682:-1
> MIGLVGKKVGMTRIFTEDGVSIPVTVIEIEANRVTQVKGLENDGYTAIQVTTGAKKANRVTKPAAGHFAKAGVEAGRGLWEFRTAEGAEFTVGQSINVDIFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQLGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA
> >ID:WP_004160595.1|Erwinia_amylovora_01SFR-BO|01SFR-BO|50S_ribosomal_protei..|630|NZ_CAPA01000010(58437):26053-26682:-1
> MIGLVGKKVGMTRIFTEDGVSIPVTVIEIEANRVTQVKGLENDGYTAIQVTTGAKKANRVTKPAAGHFAKAGVEAGRGLWEFRTAEGAEFTVGQSINVDIFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQLGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA

Answer 1

你打错了。

if letters in str(record.seq):

而不是

if letter in str(record.seq)

因此，您的检查总是失败，并为每个字母打印 else 部分。

Answer 2

我认为您想要做的是用 'X'.

替换模棱两可的 IUPAC amino acid codes（加上您不知何故获得的一些额外的字母？）

最好使用 str.translate()（在 Python 3 中）一次完成所有替换。此外，由于您正在使用 Biopython 读取文件，因此您也可以使用 Biopython 轻松编写输出文件。

from Bio import SeqIO
from Bio.Seq import Seq

letters = ["B", "Z", "J", "U", "O"]
trans_tab = str.maketrans(''.join(letters), 'X'*len(letters))

def yield_seqs(in_file):
    for record in SeqIO.parse(in_file, 'fasta'):
        record.seq = Seq(str(record.seq).translate(trans_tab))
        yield record

SeqIO.write(yield_seqs('input.fasta'), 'output.fasta', 'fasta')

示例：

$ cat input.fasta 
>1
MBZJ
$ python3 myscript.py
$ cat output.fasta 
>1
MXXX

使用字符列表在输出中重复写入 - python

Repetitive writing in output using list of characters - python

python

bioinformatics

fasta

biopython