57 lines
1.8 KiB
Python
57 lines
1.8 KiB
Python
#!/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
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homedir = os.path.expanduser('~')
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os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
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from submit_dynamut import *
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########################################################################
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# variables
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my_host = 'http://biosig.unimelb.edu.au'
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my_prediction_url = f"{my_host}/dynamut/prediction_list"
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print(my_prediction_url)
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# TODO: add cmd line args
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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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my_chain = 'A'
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my_email = 'tanushree.tunstall@lshtm.ac.uk'
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my_pdb_file = indir + '/gid_complex.pdb'
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#==============================================================================
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# batch 8: 07.txt, # RAN: 22 Feb 09:26
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#my_mutation_list = outdir + '/snp_batches/50/snp_batch_07.txt'
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#my_suffix = 'gid_b8'
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# batch 9: 08.txt, # RAN: 22 Feb 09:26
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#my_mutation_list = outdir + '/snp_batches/50/snp_batch_08.txt'
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#my_suffix = 'gid_b9'
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# batch 10: 09.txt, # RAN:22 Feb 09:26
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my_mutation_list = outdir + '/snp_batches/50/snp_batch_09.txt'
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my_suffix = 'gid_b10'
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#==============================================================================
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#==========================
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# CALL: submit_dynamut()
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# Data: gid+streptomycin
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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 = outdir
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, outfile_suffix = my_suffix)
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#%%#####################################################################
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