首先,我要明确地说我是编程方面的超级新手。 我有2个zip文件(每个文件包含一个数据库)和4个fasta文件(每个文件包含三个蛋白质序列,一个文件包含一个核苷酸序列)。
我想创建一个程序,用户可以从菜单中选择一个程序,以针对其数据库分别运行氨基酸或核苷酸文件。下面提到的代码是我能够做到的最好的代码。不幸的是,它根本没有运行。如果您能指导我如何处理我,我将非常有责任。
import sys
import zipfile
def main():
def menu():
print("*****MAIN MENU*****")`
print()
choice = input("""
A: For nucleotide "DNA" quest
B: For amino acid "Protein" quest
Q: For Exit the program
Please enter your choice: """)
if choice == "A" or choice =="a":
Dnaquery()
elif choice == "B" or choice =="b":
Proteinquery()
elif choice=="Q" or choice=="q":
sys.exit
else:
print("You must only select either A,B,or Q.")
print("Please try again")
menu()
def Dnaquery(): #for nucletide query
with zipfile.ZipFile("Dna.zip","r") as zip_ref:
zip_ref.extractall("C:\Users\Gpapa\Desktop\Zipfiles\DnaDatabase>")
from Bio.Blast import NCBIWWW
fasta_string = open("Dna.fasta").read()
result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)
def Proteinquery(): #for protein query
with zipfile.ZipFile("Protein.zip","r") as zip_ref:
zip_ref.extractall("C:\Users\Gpapa\Desktop\Zipfiles\ProteinDatabase>")
def menu2 ()
print("************Select Protein 2 blast **************")
print()
choice = input("""
1: For Protein Query 1
2: For Protein Query 2
3: For Protein Query 3
Please enter your choice: """)
if choice == 1:
from Bio.Blast import NCBIWWW
fasta_string = open("protein1.fasta").read()
result_handle = NCBIWWW.qblast("blastp", "prot", fasta_string)
elif choice == 2:
from Bio.Blast import NCBIWWW
fasta_string = open("protein2.fasta").read()
result_handle = NCBIWWW.qblast("blastp", "prot", fasta_string)
elif choice==3:
from Bio.Blast import NCBIWWW
fasta_string = open("protein3.fasta").read()
result_handle = NCBIWWW.qblast("blastp", "prot", fasta_string)
else:
print("You must only select either 1,2,or 3")
print("Please try again")
menu2()
main()
答案 0 :(得分:0)
您似乎是BLASTING NCBI,而不是本地BLAST。我建议您从这里开始进行本地BLAST:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download