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saving dynamut and mcsm_na jobs submitted and retrieved

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This commit is contained in:
Tanushree Tunstall 2021-08-11 17:32:15 +01:00
parent 93482df47a
commit cf0db2a9c0
13 changed files with 32 additions and 119 deletions
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27
dynamut/run_submit_dynamut.py Normal file → Executable file
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@ -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)
#%%#####################################################################