56 lines
1.8 KiB
Python
Executable file
56 lines
1.8 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 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/mcsm_na')
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from submit_mcsm_na import *
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from get_results_mcsm_na import *
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#%%#####################################################################
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#EXAMPLE RUN for different stages
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#=====================
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# STAGE: submit_mcsm_na.py
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#=====================
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my_host = 'http://biosig.unimelb.edu.au'
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my_prediction_url = f"{my_host}/mcsm_na/run_prediction_list"
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print(my_prediction_url)
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my_outdir = homedir + '/git/LSHTM_analysis/mcsm_na'
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my_nuc_type = 'RNA'
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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/mcsm_na/test_snps_b1.csv'
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my_suffix = 'TEST'
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#----------------------------------------------
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# example 1: 2 snps in a file
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#----------------------------------------------
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submit_mcsm_na(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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, nuc_type = my_nuc_type
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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/mcsm_na'
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#----------------------------------------------
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# example 1: single url in a single file
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#----------------------------------------------
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my_url_file_single = homedir + '/git/LSHTM_analysis/mcsm_na/mcsm_na_temp/mcsm_na_result_url_gid_test_b1.txt'
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print(my_url_file_single)
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my_suffix = 'single'
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get_results(url_file = 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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