60 lines
1.9 KiB
Python
Executable file
60 lines
1.9 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
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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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outdir_dynamut = outdir + 'dynamut_results/'
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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 7: 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_b7'
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# batch 8: 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_b8'
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# batch 9 and 10 failed!
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# bissecting: b10, split into 5 (1st failed, 2nd worked, but then comb rest)
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my_mutation_list = outdir + 'snp_batches/50/b9_b10_bissect/b10_21.txt'
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my_suffix = 'gid_b10_21'
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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_dynamut
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, outfile_suffix = my_suffix)
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#%%#####################################################################
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