saving dynamut and mcsm_na jobs submitted and retrieved
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13 changed files with 32 additions and 119 deletions
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mutationinformation,ddg_dynamut,ddg_encom,ddg_mcsm,ddg_sdm,ddg_duet,dds_encom
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G13V,0.006 kcal/mol (Stabilizing),-0.053 kcal/mol (Destabilizing),-0.261 kcal/mol (Destabilizing),-0.120 kcal/mol (Destabilizing),0.120 kcal/mol (Stabilizing),0.066 kcal.mol-1.K-1 (Increase of molecule flexibility)
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A19T,-0.077 kcal/mol (Destabilizing),0.224 kcal/mol (Destabilizing),-0.631 kcal/mol (Destabilizing),-2.620 kcal/mol (Destabilizing),-0.758 kcal/mol (Destabilizing),-0.280 kcal.mol-1.K-1 (Decrease of molecule flexibility)
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I4N,-0.239 kcal/mol (Destabilizing),-0.720 kcal/mol (Destabilizing),-0.728 kcal/mol (Destabilizing),-0.550 kcal/mol (Destabilizing),-0.461 kcal/mol (Destabilizing),0.900 kcal.mol-1.K-1 (Increase of molecule flexibility)
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P3S,0.727 kcal/mol (Stabilizing),0.334 kcal/mol (Destabilizing),-0.672 kcal/mol (Destabilizing),0.010 kcal/mol (Stabilizing),-0.252 kcal/mol (Destabilizing),-0.418 kcal.mol-1.K-1 (Decrease of molecule flexibility)
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F12S,-0.270 kcal/mol (Destabilizing),0.048 kcal/mol (Destabilizing),-1.028 kcal/mol (Destabilizing),-0.930 kcal/mol (Destabilizing),-0.993 kcal/mol (Destabilizing),-0.060 kcal.mol-1.K-1 (Decrease of molecule flexibility)
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A19V,2.389 kcal/mol (Stabilizing),0.450 kcal/mol (Destabilizing),0.659 kcal/mol (Stabilizing),-0.170 kcal/mol (Destabilizing),1.040 kcal/mol (Stabilizing),-0.562 kcal.mol-1.K-1 (Decrease of molecule flexibility)
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mutationinformation,ddg_dynamut,ddg_encom,ddg_mcsm,ddg_sdm,ddg_duet,dds_encom
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G13V,0.006 kcal/mol (Stabilizing),-0.053 kcal/mol (Destabilizing),-0.261 kcal/mol (Destabilizing),-0.120 kcal/mol (Destabilizing),0.120 kcal/mol (Stabilizing),0.066 kcal.mol-1.K-1 (Increase of molecule flexibility)
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A19T,-0.077 kcal/mol (Destabilizing),0.224 kcal/mol (Destabilizing),-0.631 kcal/mol (Destabilizing),-2.620 kcal/mol (Destabilizing),-0.758 kcal/mol (Destabilizing),-0.280 kcal.mol-1.K-1 (Decrease of molecule flexibility)
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http://biosig.unimelb.edu.au/dynamut/results_prediction/161296287365
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http://biosig.unimelb.edu.au/dynamut/results_prediction/161296143994
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http://biosig.unimelb.edu.au/dynamut/results_prediction/161296201195
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http://biosig.unimelb.edu.au/dynamut/results_prediction/161296287365
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#!/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 submit_dynamut import *
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from get_results_dynamut 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"{my_host}/dynamut/prediction_list"
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print(my_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/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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4
dynamut/get_results_dynamut.py
Normal file → Executable file
4
dynamut/get_results_dynamut.py
Normal file → Executable file
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@ -67,7 +67,7 @@ def get_results(url_file, host_url, output_dir, outfile_suffix):
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#============================
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# Writing results file: csv
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#============================
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dynamut_results_dir = output_dir + '/dynamut_results'
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dynamut_results_dir = output_dir + 'dynamut_results/'
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if not os.path.exists(dynamut_results_dir):
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print('\nCreating dir: dynamut_results within:', output_dir )
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os.makedirs(dynamut_results_dir)
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@ -79,7 +79,7 @@ def get_results(url_file, host_url, output_dir, outfile_suffix):
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#dynamut_results_out_df.to_csv('/tmp/test_dynamut.csv', index = False)
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# build out filename
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out_filename = dynamut_results_dir + '/dynamut_output_' + outfile_suffix + '.csv'
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out_filename = dynamut_results_dir + 'dynamut_output_' + outfile_suffix + '.csv'
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dynamut_results_out_df.to_csv(out_filename, index = False)
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# TODO: add as a cmd option
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23
dynamut/run_get_results_dynamut.py
Normal file → Executable file
23
dynamut/run_get_results_dynamut.py
Normal file → Executable file
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@ -19,23 +19,20 @@ my_host = 'http://biosig.unimelb.edu.au'
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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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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_temp = datadir + drug + '/output/dynamut_results/dynamut_temp/'
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#==============================================================================
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# batch 8: 07.txt, # RETRIEVED 23 Feb 08:54
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# batch 8: 08.txt, # RETRIEVED 23 Feb 08:54
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#my_url_file = outdir + '/dynamut_temp/dynamut_result_url_gid_b8.txt'
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#my_suffix = 'gid_b8'
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#my_suffix = 'gid_b7'
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# batch 9: 08.txt, # RETRIEVED 23 Feb 08:55
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my_url_file = outdir + '/dynamut_temp/dynamut_result_url_gid_b9.txt'
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my_suffix = 'gid_b9'
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# batch 10: 09.txt, # RETRIEVED
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#my_url_file = outdir + '/dynamut_temp/dynamut_result_url_gid_b10.txt'
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#my_suffix = 'gid_b10'
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#b09 and b10 failed!
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# batch 9: 09.txt,
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my_url_file = outdir_dynamut_temp + 'dynamut_result_url_gid_b10_ab.txt'
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my_suffix = 'gid_b10_ab'
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#==============================================================================
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#==========================
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27
dynamut/run_submit_dynamut.py
Normal file → Executable file
27
dynamut/run_submit_dynamut.py
Normal file → Executable file
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@ -19,27 +19,30 @@ 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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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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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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# 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: 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 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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# 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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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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@ -52,6 +55,6 @@ submit_dynamut(host_url = my_host
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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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, output_dir = outdir_dynamut
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, outfile_suffix = my_suffix)
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#%%#####################################################################
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F12S
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A19V
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G13V
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A19T
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@ -16,3 +16,4 @@ split ../../${INFILE} -l ${CHUNK} -d snp_batch_
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# use case
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#~/git/LSHTM_analysis/dynamut/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50
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#~/git/LSHTM_analysis/dynamut/split_csv.sh embb_mcsm_formatted_snps.csv snp_batches 50
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4
dynamut/submit_dynamut.py
Normal file → Executable file
4
dynamut/submit_dynamut.py
Normal file → Executable file
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@ -74,12 +74,12 @@ def submit_dynamut(host_url
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#===============
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# writing file: result urls
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#===============
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dynamut_temp_dir = output_dir + '/dynamut_temp' # creates a temp dir within output_dir
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dynamut_temp_dir = output_dir + 'dynamut_temp/' # creates a temp dir within output_dir
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if not os.path.exists(dynamut_temp_dir):
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print('\nCreating dynamut_temp in output_dir', output_dir )
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os.makedirs(dynamut_temp_dir)
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out_url_file = dynamut_temp_dir + '/dynamut_result_url_' + str(outfile_suffix) + '.txt'
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out_url_file = dynamut_temp_dir + 'dynamut_result_url_' + str(outfile_suffix) + '.txt'
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print('\nWriting output url file:', out_url_file)
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myfile = open(out_url_file, 'a')
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myfile.write(url)
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@ -22,6 +22,7 @@ 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_mcsm_na = outdir + 'mcsm_na_results'
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my_nuc_type = 'RNA'
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my_pdb_file = indir + '/gid_complex.pdb'
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@ -43,6 +44,6 @@ submit_mcsm_na(host_url = my_host
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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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, output_dir = outdir_mcsm_na
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, outfile_suffix = my_suffix)
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#%%#####################################################################
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