46 lines
No EOL
1.4 KiB
Python
Executable file
46 lines
No EOL
1.4 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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#%% 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/mcsm_na')
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from submit_mcsm_na 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}/mcsm_na/run_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_nuc_type = 'RNA'
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my_pdb_file = indir + '/gid_complex.pdb'
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#=============================================================================
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# batch 26: 25.txt # RAN: 16 Feb:
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my_mutation_list = outdir + '/snp_batches/20/snp_batch_25.txt'
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my_suffix = 'gid_b26'
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#==============================================================================
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#==========================
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# CALL: submit_mcsm_na()
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# Data: gid+streptomycin
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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 = outdir
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, outfile_suffix = my_suffix)
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#%%##################################################################### |