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