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Python NCBIWWW (Hanging Load)


Good Evening StackOverflow Pham,

I'm attempting to use Biopython's functionality for NCBIWWW to find quick <750 protein-peptide alignments. The problem I'm bumping into seems to be a hanging load when launching my program. See my code below:

import Bio
from Bio import Seq
from Bio.Blast import NCBIWWW
import tkinter as tk
from tkinter import filedialog

# Use filedialog to locate txt file for query
protein_file = filedialog.askopenfilename()
print(protein_file)

# Parse the txt file, opening and read to VERIFY grab
protein_file = open(protein_file)
protein_read = protein_file.read()
print(protein_read)

# Take query and run to determine homologous alignments of like proteins
result_handle = NCBIWWW.qblast("blastp", "nt", protein_read)
result_handle = result_handle.open('r')
print(result_handle)

Once I run the program (Ctrl + Shift + F10), the first time IT WORKED! But now, it just hangs for hours. To solve this, I begun reading through the Biopython Cookbook to find out why my code wasn't working. Here is what I tried.

  1. Verify Syntax
  2. Rewrite Code

I've attached a screenshot to hopefully provide further context... but I'm genuinely lost.

Screenshot of my Pycharm on infinite HANG

Any suggestions?

Thank you SO Team!

~ D


Solution

  • Answer is found from @Chris_Rands

    Problem Found - Calling database of "nt" should be database "nr"

    Closing request!