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testing dynamut script

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Tanushree Tunstall 2021-02-09 18:28:16 +00:00
parent aec61e2c1f
commit d77491b507
1 changed files with 15 additions and 11 deletions
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28
dynamut/dynamut_test.py
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@ -19,13 +19,17 @@ import pandas as pd
from pandas.api.types import is_string_dtype from pandas.api.types import is_string_dtype
from pandas.api.types import is_numeric_dtype from pandas.api.types import is_numeric_dtype
#%%============================================================================ #%%============================================================================
#streptomycin/gid_complex.pdb
host_dynamut = 'http://biosig.unimelb.edu.au/dynamut'
pred_dynamut_batch = '/results_prediction/161287964015'
result_id = re.search( r"([0-9]+)$", pred_dynamut).group(0)
batch_result_url = 'http://biosig.unimelb.edu.au/dynamut/results_prediction/15955901077' batch_result_url = host_dynamut + pred_dynamut_batch
mut = 'S104R'
single_result_url = 'http://biosig.unimelb.edu.au/dynamut/single_results/15955901077' + '/' + mut
mut = 'S2C'
single_url = host_dynamut + '/single_results/' + str(result_id)
single_result_url = host_dynamut + '/single_results/' + str(result_id) + '/' + mut
print(single_result_url)
#%%============================================================================ #%%============================================================================
param_dict = {} param_dict = {}
@ -54,20 +58,20 @@ if result_response.status_code == 200:
} }
results_df = pd.DataFrame.from_dict(param_dict, orient = "index").T results_df = pd.DataFrame.from_dict(param_dict, orient = "index").T
#%% for loop print(results_df)
#%%
host_dynamut = 'http://biosig.unimelb.edu.au/dynamut'
batch_url_number = re.search(r'([0-9]+)$', batch_result_url).group(0)
single_url = host_dynamut + '/single_results/' + batch_url_number
muts = ["S104R", "G24R"] #%% for loop
single_url = host_dynamut + '/single_results/' + str(result_id)
muts = ["S2C", "S2F"]
# initilialise empty df # initilialise empty df
dynamut_results_df = pd.DataFrame() dynamut_results_df = pd.DataFrame()
for i, mut in enumerate(muts): for i, mut in enumerate(muts):
#param_dict = {} #param_dict = {}
print('Running mutation', i, ':', mut) print('Running mutation', i+1, ':', mut)
snp = mut snp = mut
single_result_url = single_url + '/' + snp single_result_url = single_url + '/' + snp
print('Getting results from:', single_result_url) print('Getting results from:', single_result_url)