96 lines
2.9 KiB
Python
Executable file
96 lines
2.9 KiB
Python
Executable file
#!/usr/bin/env python3
|
|
# -*- coding: utf-8 -*-
|
|
"""
|
|
Created on Wed Aug 19 14:33:51 2020
|
|
|
|
@author: tanu
|
|
"""
|
|
#%% load packages
|
|
import os,sys
|
|
import subprocess
|
|
import argparse
|
|
import requests
|
|
import re
|
|
import time
|
|
from bs4 import BeautifulSoup
|
|
import pandas as pd
|
|
from pandas.api.types import is_string_dtype
|
|
from pandas.api.types import is_numeric_dtype
|
|
#%% homedir
|
|
homedir = os.path.expanduser('~')
|
|
print('My homedir is:', homedir)
|
|
|
|
#%%
|
|
host = 'http://biosig.unimelb.edu.au'
|
|
prediction_url = f"{host}/dynamut/prediction_list"
|
|
print(prediction_url)
|
|
|
|
#%% example params
|
|
gene_name = 'gid'
|
|
drug = 'streptomycin'
|
|
datadir = homedir + '/git/Data'
|
|
indir = datadir + '/' + drug + '/input'
|
|
#outdir = datadir + '/' + drug + '/output'
|
|
outdir = homedir + '/git/LSHTM_analysis/dynamut' # for example
|
|
|
|
dynamut_temp_dir = outdir + '/dynamut_temp'
|
|
|
|
if not os.path.exists(dynamut_temp_dir):
|
|
print('Creating dynamut_temp in outdir', outdir )
|
|
os.makedirs(dynamut_temp_dir)
|
|
|
|
batch_no = 1
|
|
out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
|
|
|
|
|
|
#%% request calculation (no def)
|
|
with open("/home/tanu/git/Data/streptomycin/input/gid_complex.pdb", "rb") as pdb_file, open ("/home/tanu/git/LSHTM_analysis/dynamut/snp_test2.csv") as mutation_list:
|
|
files = {"wild": pdb_file
|
|
, "mutation_list": mutation_list}
|
|
body = {"chain": 'A'
|
|
, "email": 'tanushree.tunstall@lshtm.ac.uk'}
|
|
|
|
response = requests.post(prediction_url, files = files, data = body)
|
|
print(response.status_code)
|
|
if response.history:
|
|
print('PASS: valid mutation submitted. Fetching result url')
|
|
url_match = re.search('/dynamut/results_prediction/.+(?=")', response.text)
|
|
url = host + url_match.group()
|
|
print(url)
|
|
#===============
|
|
# writing file: result urls
|
|
#===============
|
|
out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
|
|
print('Writing output url file:', out_url_file)
|
|
myfile = open(out_url_file, 'a')
|
|
myfile.write(url)
|
|
myfile.close()
|
|
|
|
#%%
|
|
def request_calculation(pdb_file, mutation_list
|
|
, chain
|
|
, my_email
|
|
, prediction_url
|
|
, output_dir
|
|
, gene_name
|
|
, batch_no
|
|
, out_url_file):
|
|
"""
|
|
Makes a POST request for a ligand affinity prediction.
|
|
|
|
@param pdb_file: valid path to pdb structure
|
|
@type string
|
|
|
|
@param mutation_list: list of mutations (1 per line) of the format: {WT}<POS>{Mut}
|
|
@type string
|
|
|
|
@param chain: single-letter(caps)
|
|
@type chr
|
|
|
|
@param prediction_url: dynamut url for prediction
|
|
@type string
|
|
|
|
@return response object
|
|
@type object
|
|
"""
|
|
#====================
|