From 96277d78f69d8d6138932301787359e5815e1b96 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Wed, 11 Aug 2021 17:32:15 +0100 Subject: [PATCH] saving dynamut and mcsm_na jobs submitted and retrieved --- .../dynamut_output_multiple.csv | 7 -- .../dynamut_results/dynamut_output_single.csv | 3 - .../dynamut_result_url_batch_multiple.txt | 3 - .../dynamut_result_url_batch_single.txt | 1 - dynamut/examples.py | 71 ------------------- dynamut/get_results_dynamut.py | 4 +- dynamut/run_get_results_dynamut.py | 23 +++--- dynamut/run_submit_dynamut.py | 27 +++---- dynamut/snp_test1.csv | 2 - dynamut/snp_test2.csv | 2 - dynamut/split_csv.sh | 1 + dynamut/submit_dynamut.py | 4 +- mcsm_na/run_submit_mcsm_na.py | 3 +- 13 files changed, 32 insertions(+), 119 deletions(-) delete mode 100644 dynamut/dynamut_results/dynamut_output_multiple.csv delete mode 100644 dynamut/dynamut_results/dynamut_output_single.csv delete mode 100644 dynamut/dynamut_temp/dynamut_result_url_batch_multiple.txt delete mode 100644 dynamut/dynamut_temp/dynamut_result_url_batch_single.txt delete mode 100644 dynamut/examples.py mode change 100644 => 100755 dynamut/get_results_dynamut.py mode change 100644 => 100755 dynamut/run_get_results_dynamut.py mode change 100644 => 100755 dynamut/run_submit_dynamut.py delete mode 100644 dynamut/snp_test1.csv delete mode 100644 dynamut/snp_test2.csv mode change 100644 => 100755 dynamut/submit_dynamut.py diff --git a/dynamut/dynamut_results/dynamut_output_multiple.csv b/dynamut/dynamut_results/dynamut_output_multiple.csv deleted file mode 100644 index fef0be4..0000000 --- a/dynamut/dynamut_results/dynamut_output_multiple.csv +++ /dev/null @@ -1,7 +0,0 @@ -mutationinformation,ddg_dynamut,ddg_encom,ddg_mcsm,ddg_sdm,ddg_duet,dds_encom -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) -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) -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) -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) -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) -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) diff --git a/dynamut/dynamut_results/dynamut_output_single.csv b/dynamut/dynamut_results/dynamut_output_single.csv deleted file mode 100644 index b117494..0000000 --- a/dynamut/dynamut_results/dynamut_output_single.csv +++ /dev/null @@ -1,3 +0,0 @@ -mutationinformation,ddg_dynamut,ddg_encom,ddg_mcsm,ddg_sdm,ddg_duet,dds_encom -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) -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) diff --git a/dynamut/dynamut_temp/dynamut_result_url_batch_multiple.txt b/dynamut/dynamut_temp/dynamut_result_url_batch_multiple.txt deleted file mode 100644 index 592e2d8..0000000 --- a/dynamut/dynamut_temp/dynamut_result_url_batch_multiple.txt +++ /dev/null @@ -1,3 +0,0 @@ -http://biosig.unimelb.edu.au/dynamut/results_prediction/161296287365 -http://biosig.unimelb.edu.au/dynamut/results_prediction/161296143994 -http://biosig.unimelb.edu.au/dynamut/results_prediction/161296201195 diff --git a/dynamut/dynamut_temp/dynamut_result_url_batch_single.txt b/dynamut/dynamut_temp/dynamut_result_url_batch_single.txt deleted file mode 100644 index 7b27943..0000000 --- a/dynamut/dynamut_temp/dynamut_result_url_batch_single.txt +++ /dev/null @@ -1 +0,0 @@ -http://biosig.unimelb.edu.au/dynamut/results_prediction/161296287365 diff --git a/dynamut/examples.py b/dynamut/examples.py deleted file mode 100644 index a063384..0000000 --- a/dynamut/examples.py +++ /dev/null @@ -1,71 +0,0 @@ -#!/usr/bin/env python3 -# -*- coding: utf-8 -*- -""" -Created on Fri Feb 12 12:15:26 2021 - -@author: tanu -""" -import os -homedir = os.path.expanduser('~') -os.chdir (homedir + '/git/LSHTM_analysis/dynamut') -from submit_dynamut import * -from get_results_dynamut import * -#%%##################################################################### -#EXAMPLE RUN for different stages -#===================== -# STAGE: submit.py -#===================== -my_host = 'http://biosig.unimelb.edu.au' -my_prediction_url = f"{my_host}/dynamut/prediction_list" -print(my_prediction_url) - -my_outdir = homedir + '/git/LSHTM_analysis/dynamut' -my_chain = 'A' -my_email = 'tanushree.tunstall@lshtm.ac.uk' - -my_pdb_file = homedir + '/git/Data/streptomycin/input/gid_complex.pdb' -my_mutation_list = homedir + '/git/LSHTM_analysis/dynamut/snp_test1.csv' -my_suffix = 'gid_test1' - -#---------------------------------------------- -# example 1: 2 snps in a file -#---------------------------------------------- -submit_dynamut(host_url = my_host -, pdb_file = my_pdb_file -, mutation_list = my_mutation_list -, chain = my_chain -, email_address = my_email -, prediction_url = my_prediction_url -, output_dir = my_outdir -, outfile_suffix = my_suffix) -#%%################################################################### -#===================== -# STAGE: get_results.py -#===================== -my_host = 'http://biosig.unimelb.edu.au' -my_outdir = homedir + '/git/LSHTM_analysis/dynamut' - -#---------------------------------------------- -# example 1: multiple urls in a single file -#---------------------------------------------- -my_url_file_multiple = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_multiple.txt' -print(my_url_file_multiple) -my_suffix = 'multiple' - -get_results(url_file = my_url_file_multiple - , host_url = my_host - , output_dir = my_outdir - , outfile_suffix = my_suffix) - -#---------------------------------------------- -# example 2: single url in a file -#---------------------------------------------- -my_url_file_single = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_single.txt' -print(my_url_file_single) -my_suffix = 'single' - -get_results(my_url_file_single - , host_url = my_host - , output_dir = my_outdir - , outfile_suffix = my_suffix) -#%%################################################################### diff --git a/dynamut/get_results_dynamut.py b/dynamut/get_results_dynamut.py old mode 100644 new mode 100755 index 4fa924c..d79c4f1 --- a/dynamut/get_results_dynamut.py +++ b/dynamut/get_results_dynamut.py @@ -67,7 +67,7 @@ def get_results(url_file, host_url, output_dir, outfile_suffix): #============================ # Writing results file: csv #============================ - dynamut_results_dir = output_dir + '/dynamut_results' + dynamut_results_dir = output_dir + 'dynamut_results/' if not os.path.exists(dynamut_results_dir): print('\nCreating dir: dynamut_results within:', output_dir ) os.makedirs(dynamut_results_dir) @@ -79,7 +79,7 @@ def get_results(url_file, host_url, output_dir, outfile_suffix): #dynamut_results_out_df.to_csv('/tmp/test_dynamut.csv', index = False) # build out filename - out_filename = dynamut_results_dir + '/dynamut_output_' + outfile_suffix + '.csv' + out_filename = dynamut_results_dir + 'dynamut_output_' + outfile_suffix + '.csv' dynamut_results_out_df.to_csv(out_filename, index = False) # TODO: add as a cmd option diff --git a/dynamut/run_get_results_dynamut.py b/dynamut/run_get_results_dynamut.py old mode 100644 new mode 100755 index fd4b5a1..872b03e --- a/dynamut/run_get_results_dynamut.py +++ b/dynamut/run_get_results_dynamut.py @@ -19,23 +19,20 @@ my_host = 'http://biosig.unimelb.edu.au' # TODO: add cmd line args #gene = 'gid' drug = 'streptomycin' -datadir = homedir + '/git/Data' -indir = datadir + '/' + drug + '/input' -outdir = datadir + '/' + drug + '/output' - +datadir = homedir + '/git/Data/' +indir = datadir + drug + '/input/' +outdir = datadir + drug + '/output/' +outdir_dynamut_temp = datadir + drug + '/output/dynamut_results/dynamut_temp/' #============================================================================== -# batch 8: 07.txt, # RETRIEVED 23 Feb 08:54 +# batch 8: 08.txt, # RETRIEVED 23 Feb 08:54 #my_url_file = outdir + '/dynamut_temp/dynamut_result_url_gid_b8.txt' -#my_suffix = 'gid_b8' +#my_suffix = 'gid_b7' -# batch 9: 08.txt, # RETRIEVED 23 Feb 08:55 -my_url_file = outdir + '/dynamut_temp/dynamut_result_url_gid_b9.txt' -my_suffix = 'gid_b9' - -# batch 10: 09.txt, # RETRIEVED -#my_url_file = outdir + '/dynamut_temp/dynamut_result_url_gid_b10.txt' -#my_suffix = 'gid_b10' +#b09 and b10 failed! +# batch 9: 09.txt, +my_url_file = outdir_dynamut_temp + 'dynamut_result_url_gid_b10_ab.txt' +my_suffix = 'gid_b10_ab' #============================================================================== #========================== diff --git a/dynamut/run_submit_dynamut.py b/dynamut/run_submit_dynamut.py old mode 100644 new mode 100755 index ce67cbc..6408a4e --- a/dynamut/run_submit_dynamut.py +++ b/dynamut/run_submit_dynamut.py @@ -19,27 +19,30 @@ print(my_prediction_url) # TODO: add cmd line args #gene = 'gid' drug = 'streptomycin' -datadir = homedir + '/git/Data' -indir = datadir + '/' + drug + '/input' -outdir = datadir + '/' + drug + '/output' +datadir = homedir + '/git/Data/' +indir = datadir + drug + '/input/' +outdir = datadir + drug + '/output/' +outdir_dynamut = outdir + 'dynamut_results/' my_chain = 'A' my_email = 'tanushree.tunstall@lshtm.ac.uk' -my_pdb_file = indir + '/gid_complex.pdb' +my_pdb_file = indir + 'gid_complex.pdb' #============================================================================== -# batch 8: 07.txt, # RAN: 22 Feb 09:26 +# batch 7: 07.txt, # RAN: 22 Feb 09:26 #my_mutation_list = outdir + '/snp_batches/50/snp_batch_07.txt' +#my_suffix = 'gid_b7' + +# batch 8: 08.txt, # RAN: 22 Feb 09:26 +#my_mutation_list = outdir + '/snp_batches/50/snp_batch_08.txt' #my_suffix = 'gid_b8' -# batch 9: 08.txt, # RAN: 22 Feb 09:26 -#my_mutation_list = outdir + '/snp_batches/50/snp_batch_08.txt' -#my_suffix = 'gid_b9' +# batch 9 and 10 failed! +# bissecting: b10, split into 5 (1st failed, 2nd worked, but then comb rest) -# batch 10: 09.txt, # RAN:22 Feb 09:26 -my_mutation_list = outdir + '/snp_batches/50/snp_batch_09.txt' -my_suffix = 'gid_b10' +my_mutation_list = outdir + 'snp_batches/50/b9_b10_bissect/b10_21.txt' +my_suffix = 'gid_b10_21' #============================================================================== #========================== @@ -52,6 +55,6 @@ submit_dynamut(host_url = my_host , chain = my_chain , email_address = my_email , prediction_url = my_prediction_url - , output_dir = outdir + , output_dir = outdir_dynamut , outfile_suffix = my_suffix) #%%##################################################################### diff --git a/dynamut/snp_test1.csv b/dynamut/snp_test1.csv deleted file mode 100644 index 9e179c2..0000000 --- a/dynamut/snp_test1.csv +++ /dev/null @@ -1,2 +0,0 @@ -F12S -A19V diff --git a/dynamut/snp_test2.csv b/dynamut/snp_test2.csv deleted file mode 100644 index e72171c..0000000 --- a/dynamut/snp_test2.csv +++ /dev/null @@ -1,2 +0,0 @@ -G13V -A19T diff --git a/dynamut/split_csv.sh b/dynamut/split_csv.sh index 5e7bfd9..b5f15f1 100755 --- a/dynamut/split_csv.sh +++ b/dynamut/split_csv.sh @@ -16,3 +16,4 @@ split ../../${INFILE} -l ${CHUNK} -d snp_batch_ # use case #~/git/LSHTM_analysis/dynamut/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50 +#~/git/LSHTM_analysis/dynamut/split_csv.sh embb_mcsm_formatted_snps.csv snp_batches 50 diff --git a/dynamut/submit_dynamut.py b/dynamut/submit_dynamut.py old mode 100644 new mode 100755 index 2c66d90..37e03be --- a/dynamut/submit_dynamut.py +++ b/dynamut/submit_dynamut.py @@ -74,12 +74,12 @@ def submit_dynamut(host_url #=============== # writing file: result urls #=============== - dynamut_temp_dir = output_dir + '/dynamut_temp' # creates a temp dir within output_dir + dynamut_temp_dir = output_dir + 'dynamut_temp/' # creates a temp dir within output_dir if not os.path.exists(dynamut_temp_dir): print('\nCreating dynamut_temp in output_dir', output_dir ) os.makedirs(dynamut_temp_dir) - out_url_file = dynamut_temp_dir + '/dynamut_result_url_' + str(outfile_suffix) + '.txt' + out_url_file = dynamut_temp_dir + 'dynamut_result_url_' + str(outfile_suffix) + '.txt' print('\nWriting output url file:', out_url_file) myfile = open(out_url_file, 'a') myfile.write(url) diff --git a/mcsm_na/run_submit_mcsm_na.py b/mcsm_na/run_submit_mcsm_na.py index 474ca5c..8f7ed90 100755 --- a/mcsm_na/run_submit_mcsm_na.py +++ b/mcsm_na/run_submit_mcsm_na.py @@ -22,6 +22,7 @@ drug = 'streptomycin' datadir = homedir + '/git/Data' indir = datadir + '/' + drug + '/input' outdir = datadir + '/' + drug + '/output' +outdir_mcsm_na = outdir + 'mcsm_na_results' my_nuc_type = 'RNA' my_pdb_file = indir + '/gid_complex.pdb' @@ -43,6 +44,6 @@ submit_mcsm_na(host_url = my_host , mutation_list = my_mutation_list , nuc_type = my_nuc_type , prediction_url = my_prediction_url - , output_dir = outdir + , output_dir = outdir_mcsm_na , outfile_suffix = my_suffix) #%%#####################################################################