解析两个文件以合并数据并创建新的Fasta文件

如何解决解析两个文件以合并数据并创建新的Fasta文件

我有两个文件： human.fa 和 protein-coding_gene.txt （有数百种不同的蛋白质信息）。我必须先解析蛋白质编码基因，然后再解析human.fa（10个蛋白质名称），然后将其合并到一个新的fasta文件中。

protein-coding_gene.txt：

Protein1 PreviousNames1 PreviousSymbols1 Symbol1 Chromosome1
Protein2 PreviousNames2 PreviousSymbols2 Symbol2 Chromosome2

human.fa：

>Protein1  Sequence1
>Protein2 Sequence2

我需要一个新的fasta文件来输出：

>Protein1 Synonyms1 Chromsome1 Sequence1
>Protein2 Synonyms2 Chromosome2 Sequence2 

我当前的代码是：

class Protein:
    
    def __init__(self,Name,Synonyms,Chromosome):
        self.Name = Name
        self.Synonyms = Synonyms
        self.Chromosome = Chromosome
             
Proteins = []
with open('protein-coding_gene.txt','r') as file:
    for line in file:
        parseline = line.rstrip().split("\t")
        Name = parseline[2]
        Synonyms = parseline[6]
        Chromosome = parseline[7]
        Proteins.append(Protein(Name,Chromosome))


f = open("human.fa")

seqs = {}
for i in f:
    line = i.strip()
    if line[0] == '>':
        l = line.split()
        gene = l[0][1:]
        seqs[gene] = ''
    else:
        seqs[gene] = seqs[gene] + line

        
f.close()

        
for p in Proteins:
    print(p.Name,p.Synonyms,p.Chromosome,sep=",")

for name,seq in seqs.items():
        print (name,seq)
        

from Bio import SeqIO
        
newhuman = []
SeqIO.write[newhuman,"fastaML.fa","fasta")

现在，它会打印我想要的蛋白质编码文件（名称，同义词，染色体）中的所有内容，并打印整个human.fa文件。我需要它来进行排序，并且仅使用来自protein-coding_gene.txt和序列的信息打印出fasta文件的10个蛋白质名称。任何帮助将不胜感激。

解决方法

您想要的格式不是有效的Fasta格式。但是，如果您仍希望在fastaML.fa中使用相同的输出，则不应使用SeqIO.write（）方法。而是应该使用基本的文件处理。

class Protein:
    
    def __init__(self,Name,Synonyms,Chromosome):
        self.Name = Name
        self.Synonyms = Synonyms
        self.Chromosome = Chromosome

    def add_sequence(self,Sequence):
        self.Sequence = Sequence
             
Proteins = []
with open('protein-coding_gene.txt','r') as file:
    for line in file:
        parseline = line.rstrip().split(" ")
        Name = parseline[0]
        Synonyms = parseline[1:4]
        Chromosome = parseline[4]
        Proteins.append(Protein(">"+Name,Chromosome))


f = open("human.fa")

seqs = {}
gene = ""
for i in f:
    line = i.strip()
    if line[0] == '>':
        l = line.split()
        gene = l[0]
        seqs[gene] = l[1]
    else:
        seqs[gene] = seqs[gene] + line

        
f.close()

for p in Proteins:
    for name,seq in seqs.items():
        if(p.Name == name):
            p.add_sequence(seq)     

with open('fastaML.fa','w') as file:
    for p in Proteins:
        file.write(p.Name + " " + p.Synonyms[0] + " " + p.Synonyms[1] + " " + p.Synonyms[2] + " " + p.Chromosome + " " + p.Sequence + "\n")
        #I have used single space here. You can modify it as per your need.

Here is a working repl for your reference。