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added shell script to format muts for mcsm NA

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Tanushree Tunstall 2021-02-12 17:38:42 +00:00
parent c99f1cac92
commit 1f72001689
5 changed files with 54 additions and 31 deletions
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8
mcsm_na/examples.py
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@ -20,10 +20,10 @@ my_prediction_url = f"{my_host}/mcsm_na/run_prediction_list"
print(my_prediction_url)
my_outdir = homedir + '/git/LSHTM_analysis/mcsm_na'
my_nuc_type = 'RNA'
my_pdb_file = homedir + '/git/Data/streptomycin/input/gid_complex.pdb'
my_mutation_list = homedir + '/git/LSHTM_analysis/mcsm_na/test_snps_b1.csv'
my_suffix = 'gid_test_b1'
my_suffix = 'TEST'
#----------------------------------------------
# example 1: 2 snps in a file
@ -31,7 +31,7 @@ my_suffix = 'gid_test_b1'
submit_mcsm_na(host_url = my_host
, pdb_file = my_pdb_file
, mutation_list = my_mutation_list
, nuc_type = 'RNA'
, nuc_type = my_nuc_type
, prediction_url = my_prediction_url
, output_dir = my_outdir
, outfile_suffix = my_suffix)
@ -53,4 +53,4 @@ my_suffix = 'single'
get_results(url_file = my_url_file_single
, host_url = my_host
, output_dir = my_outdir
, outfile_suffix = my_suffix)
, outfile_suffix = my_suffix)