added submit_def.py with example to run batch of 50
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2 changed files with 144 additions and 3 deletions
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@ -44,7 +44,7 @@ out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) +
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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") as mutation_list:
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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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@ -57,6 +57,7 @@ with open("/home/tanu/git/Data/streptomycin/input/gid_complex.pdb", "rb") as pdb
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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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@ -90,7 +91,31 @@ def request_calculation(pdb_file, mutation_list
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@param prediction_url: dynamut url for prediction
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@type string
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@return response object
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@type object
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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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116
dynamut/submit_def.py
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116
dynamut/submit_def.py
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@ -0,0 +1,116 @@
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#!/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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def request_calculation(pdb_file
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, mutation_list
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, batch_no
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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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#, out_url_file
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):
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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 batch_no: batch no so it can be added as a suffix to the the outfile
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@type int
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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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@param output_dir: output dir
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@type string
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@param gene_name: name of gene
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@type string
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#@param out_url_file: name of output file with batch no. as suffix
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@type string
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@return txt file containing batch no. of snps processed (i.e out_url_file)
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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, "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": chain
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, "email": my_email}
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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('\nPASS: valid submission. 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('\nURL for snp batch no ', str(batch_no), ':', url)
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#===============
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# writing file: result urls
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#===============
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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('\nCreating dynamut_temp in outdir', outdir )
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os.makedirs(dynamut_temp_dir)
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out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
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print('\nWriting 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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#%%globals!?
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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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#gene = '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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my_pdb_file = homedir + '/git/Data/streptomycin/input/gid_complex.pdb'
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my_mutation_list = homedir + '/git/Data/streptomycin/output/snp_batches/50/snp_batch_00.txt'
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my_chain = 'A'
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my_batch = 1
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#my_outfile = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
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# %% call this function
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request_calculation (pdb_file = my_pdb_file
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, mutation_list = my_mutation_list
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, chain = my_chain
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, my_email = 'tanushree.tunstall@lshtm.ac.uk'
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, prediction_url = f"{host}/dynamut/prediction_list"
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, output_dir = outdir
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, batch_no = my_batch)
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