tanu/LSHTM_analysis
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ran submit and get_results for one last batch for mcsm_na and did some bash formatting to get proper filenames, etc.

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Tanushree Tunstall 2021-08-06 19:09:29 +01:00
parent 4733ec9db0
commit 50cf6ca3ac
4 changed files with 38 additions and 7 deletions
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2
mcsm_na/get_results_mcsm_na.py
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@ -40,7 +40,7 @@ def get_results(url_file, host_url, output_dir, outfile_suffix):
txt_url = f"{host_url}/mcsm_na/static/results/" + prediction_number + '.txt'
print('CHECK txt url:', txt_url)
out_filename = mcsm_na_results_dir + '/' + outfile_suffix + '_output_' + prediction_number + '.txt'
out_filename = mcsm_na_results_dir + '/' + outfile_suffix + '_output_' + prediction_number + '.txt.gz'
response_txt = requests.get(txt_url, stream = True)
if response_txt.status_code == 200:
print('\nDownloading .txt:', txt_url

5
mcsm_na/run_get_results_mcsm_na.py
View file

@ -23,8 +23,9 @@ outdir = datadir + '/' + drug + '/output'
#==============================================================================
# batch 26: 25.txt, RETRIEVED: 16 Feb:
my_url_file = outdir + '/mcsm_na_temp/mcsm_na_result_url_gid_b26.txt'
my_suffix = 'gid_b26'
# batch 27: 26.txt, RETRIEVED: 6 Aug:
my_url_file = outdir + '/mcsm_na_temp/mcsm_na_result_url_gid_b27.txt'
my_suffix = 'gid_b27'
#==============================================================================

8
mcsm_na/run_submit_mcsm_na.py
View file

@ -28,8 +28,10 @@ my_pdb_file = indir + '/gid_complex.pdb'
#=============================================================================
# batch 26: 25.txt # RAN: 16 Feb:
my_mutation_list = outdir + '/snp_batches/20/snp_batch_25.txt'
my_suffix = 'gid_b26'
# batch 27: 26.txt # RAN: 6 Aug:
# off by one
my_mutation_list = outdir + '/snp_batches/20/snp_batch_26.txt'
my_suffix = 'gid_b27'
#==============================================================================
#==========================
@ -43,4 +45,4 @@ submit_mcsm_na(host_url = my_host
, prediction_url = my_prediction_url
, output_dir = outdir
, outfile_suffix = my_suffix)
#%%#####################################################################
#%%#####################################################################