使用字符列表在輸出中重復寫入-python

Question

在文件中，我要替換一些字符。

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

問題是輸出看起來像這樣，用字母寫出我所擁有的盡可能多的字符：

> >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

我認為您正在嘗試用'X'代替含糊的IUPAC氨基酸代碼 （加上您以某種方式獲得的一些其他字母？）。

最好使用str.translate() （在Python 3中）一次完成所有替換。 另外，由於您使用的是Biopython來讀取文件，因此您也可以使用Biopython輕松地編寫輸出文件。

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')

例：

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

Answer 2

你有錯字

if letters in str(record.seq):

代替

if letter in str(record.seq)

因此，您的支票總是失敗，並為每個字母打印else部分。