Biopython翻译()错误

Question

我有一份文件看起来是这样的：

Type    Variant_class   ACC_NUM dbsnp   genomic_coordinates_hg18    genomic_coordinates_hg19    HGVS_cdna   HGVS_protein    gene    disease sequence_context_hg18   sequence_context_hg19   codon_change    codon_number    intron_number   site    location    location_reference_point    author  journal vol page    year    pmid    entrezid    sift_score  sift_prediction mutpred_score
1   DM  CM920001    rs1800433   null    chr12:9232351:- NM_000014.4 NP_000005.2:p.C972Y A2M Chronicobstructivepulmonarydisease  null    CACAAAATCTTCTCCAGATGCCCTATGGCT[G/A]TGGAGAGCAGAATATGGTCCTCTTTGCTCC   TGT TAT 972 null    null    2   null    Poller  HUMGENET    88  313 1992    1370808 2   0   DAMAGING    0.594315245478036
1   DM  CM004784    rs74315453  null    chr22:43089410:-    NM_017436.4 NP_059132.1:p.M183K A4GALT  Pksynthasedeficiency(pphenotype)    null    TGCTCTCCGACGCCTCCAGGATCGCACTCA[T/A]GTGGAAGTTCGGCGGCATCTACCTGGACAC   ATG AAG 183 null    null    2   null    Steffensen  JBC 275 16723   2000    10747952    53947   0   DAMAGING    0.787878787878788

我想把第13栏和第14栏的信息翻译成相应的氨基酸。下面是我生成的脚本：

from Bio.Seq import Seq
from Bio.Alphabet import generic_dna

InFile = open("disease_mut_splitfinal.txt", 'rU')

InFile.readline()
OriginalSeq_list = []
MutSeq_list = []

import csv
with open("disease_mut_splitfinal.txt") as f:
    reader = csv.DictReader(f, delimiter= "\t")
    for row in reader: 
        OriginalSeq = row['codon_change']
        MutSeq = row['codon_number']
        region = row["genomic_coordinates_hg19"]
        gene = row["gene"]
        OriginalSeq_list.append(OriginalSeq)
        MutSeq_list.append(MutSeq)

OutputFileName = "Translated.txt"
OutputFile = open(OutputFileName, 'w')
OutputFile.write(''+region+'\t'+gene+'\n')


for i in range(0, len(OriginalSeq_list)):
    OrigSeq = OriginalSeq_list[i]
    MutSEQ = MutSeq_list[i]
    print OrigSeq
    translated_original = OrigSeq.translate()
    translated_mut= MutSEQ.translate()

    OutputFile.write("\n" + OriginalSeq_list[i]+ "\t" + str(translated_original) + "\t" +MutSeq_list[i] + "\t" + str(translated_mut)+ "\n")

但是，我一直收到这样的错误：

TypeError: translate expected at least 1 arguments, got 0

我对自己做错了什么感到不知所措。有什么建议吗？

splitfinal.txt?dl=0

(即使您没有dropbox，文件仍然可以下载)

Answer 1

您使用的是string方法" translate“，而不是biopython对象方法翻译，这正是我假设您想要做的。您需要将字符串转换为seq对象，然后进行转换。试一试

from Bio import Seq    
OrigSeq = Seq.Seq(OriginalSeq_list[i])
translated_original = OrigSeq.translate()

另一个选择

from Bio.Seq import Seq
OrigSeq = Seq(OriginalSeq_list[i])
translated_original = OrigSeq.translate()