86 lines
3 KiB
Python
86 lines
3 KiB
Python
#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Fri Feb 12 12:15:26 2021
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@author: tanu
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"""
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import os
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homedir = os.path.expanduser('~')
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os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
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from get_results import *
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from submit import *
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#%%#####################################################################
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#EXAMPLE RUN for different stages
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#=====================
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# STAGE: submit.py
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#=====================
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my_host = 'http://biosig.unimelb.edu.au'
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my_prediction_url = f"{host}/dynamut/prediction_list"
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print(prediction_url)
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my_outdir = homedir + '/git/LSHTM_analysis/dynamut'
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my_chain = 'A'
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my_email = 'tanushree.tunstall@lshtm.ac.uk'
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my_pdb_file = homedir + '/git/Data/streptomycin/input/gid_complex.pdb'
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my_mutation_list = homedir + '/git/LSHTM_analysis/dynamut/example_input/snp_test1.csv'
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my_suffix = 'gid_test1'
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#----------------------------------------------
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# example 1: 2 snps in a file
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#----------------------------------------------
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submit_dynamut(host_url = my_host
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, 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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, email_address = my_email
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, prediction_url = my_prediction_url
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, output_dir = my_outdir
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, outfile_suffix = my_suffix)
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#%%###################################################################
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#=====================
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# STAGE:get_results.py
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#=====================
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my_host = 'http://biosig.unimelb.edu.au'
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my_outdir = homedir + '/git/LSHTM_analysis/dynamut'
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#----------------------------------------------
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# example 1: multiple urls in a single file
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#----------------------------------------------
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my_url_file_multiple = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_multiple.txt'
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print(my_url_file_multiple)
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my_suffix = 'multiple'
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get_results(url_file = my_url_file_multiple
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, host_url = my_host
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, output_dir = my_outdir
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, outfile_suffix = my_suffix)
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#----------------------------------------------
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# example 2: single url in a file
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#----------------------------------------------
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my_url_file_single = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_single.txt'
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print(my_url_file_single)
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my_suffix = 'single'
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get_results(my_url_file_single
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, host_url = my_host
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, output_dir = my_outdir
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, outfile_suffix = my_suffix)
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#%%###################################################################
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url = 'http://biosig.unimelb.edu.au/dynamut/results_prediction/161296287365'
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host_url = 'http://biosig.unimelb.edu.au'
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prediction_number = re.search(r'([0-9]+$)', url).group(0)
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print(prediction_number)
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dynamut_results_dir = '/home/tanu/git/LSHTM_analysis/dynamut/dynamut_results'
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tgz_url = f"{host_url}/dynamut/results_file/results_" + prediction_number + '.tar.gz'
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print(tgz_url)
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outfile_suffix = 'foo'
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target_path = dynamut_results_dir + '/' + outfile_suffix + '_results_' + prediction_number + '.tar.gz'
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response_tgz = requests.get(tgz_url, stream = True)
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if response_tgz.status_code == 200:
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with open(target_path, 'wb') as f:
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f.write(response_tgz.raw.read())
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