tanu/LSHTM_analysis
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reran b7 since previous run file output was 0 bytes

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Tanushree Tunstall 2021-08-12 15:29:36 +01:00
parent cf0db2a9c0
commit 93fae9e5f5
2 changed files with 23 additions and 14 deletions
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19
dynamut/run_submit_dynamut.py
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@ -17,7 +17,7 @@ my_prediction_url = f"{my_host}/dynamut/prediction_list"
print(my_prediction_url) print(my_prediction_url)
# TODO: add cmd line args # TODO: add cmd line args
#gene = 'gid' gene = 'gid'
drug = 'streptomycin' drug = 'streptomycin'
datadir = homedir + '/git/Data/' datadir = homedir + '/git/Data/'
indir = datadir + drug + '/input/' indir = datadir + drug + '/input/'
@ -27,8 +27,8 @@ outdir_dynamut = outdir + 'dynamut_results/'
my_chain = 'A' my_chain = 'A'
my_email = 'tanushree.tunstall@lshtm.ac.uk' my_email = 'tanushree.tunstall@lshtm.ac.uk'
my_pdb_file = indir + 'gid_complex.pdb' #my_pdb_file = indir + 'gid_complex.pdb'
my_pdb_file = indir + gene + '_complex.pdb'
#============================================================================== #==============================================================================
# batch 7: 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_mutation_list = outdir + '/snp_batches/50/snp_batch_07.txt'
@ -40,15 +40,21 @@ my_pdb_file = indir + 'gid_complex.pdb'
# batch 9 and 10 failed! # batch 9 and 10 failed!
# bissecting: b10, split into 5 (1st failed, 2nd worked, but then comb rest) # bissecting: b10, split into 5 (1st failed, 2nd worked, but then comb rest)
# Rerunnig batch 7: 07.txt, # RAN: 12 Aug 15:22, 0 bytes file from previous run!
my_mutation_list = outdir + 'snp_batches/50/b9_b10_bissect/b10_21.txt' my_mutation_list = outdir + 'snp_batches/50/snp_batch_07.txt'
my_suffix = 'gid_b10_21' my_suffix = 'gid_b7'
#============================================================================== #==============================================================================
#========================== #==========================
# CALL: submit_dynamut() # CALL: submit_dynamut()
# Data: gid+streptomycin # Data: gid+streptomycin
#========================== #==========================
print('\nSubmitting batch for:'
, '\ndrug: ' , drug
, '\ngene: ' , gene
, '\nbatch: ' , my_suffix
, '\n\nFilename: ' , my_mutation_list)
submit_dynamut(host_url = my_host submit_dynamut(host_url = my_host
, pdb_file = my_pdb_file , pdb_file = my_pdb_file
, mutation_list = my_mutation_list , mutation_list = my_mutation_list
@ -57,4 +63,5 @@ submit_dynamut(host_url = my_host
, prediction_url = my_prediction_url , prediction_url = my_prediction_url
, output_dir = outdir_dynamut , output_dir = outdir_dynamut
, outfile_suffix = my_suffix) , outfile_suffix = my_suffix)
#%%##################################################################### #%%#####################################################################

4
dynamut/submit_dynamut.py
View file

@ -80,7 +80,9 @@ def submit_dynamut(host_url
os.makedirs(dynamut_temp_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) print('\nWriting output url file:', out_url_file
, '\nNow we wait patiently...')
myfile = open(out_url_file, 'a') myfile = open(out_url_file, 'a')
myfile.write(url) myfile.write(url)
myfile.close() myfile.close()