updating get_results_def.py
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parent
28521104f8
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7116b45bf8
2 changed files with 47 additions and 24 deletions
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@ -17,13 +17,8 @@ import pandas as pd
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from pandas.api.types import is_string_dtype
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from pandas.api.types import is_numeric_dtype
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#%%============================================================================
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homedir = os.path.expanduser('~')
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#print(homedir)
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host = 'http://biosig.unimelb.edu.au'
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# Needed if things try to block the 'requests' user agent
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#headers = {"User-Agent":"Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/83.0.4103.97 Safari/537.36"}
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#%%
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def get_results(url_file):
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def get_results(url_file, host_url, outdir, outfile_suffix):
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# initilialise empty df
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dynamut_results_out_df = pd.DataFrame()
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with open(url_file, 'r') as f:
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@ -38,7 +33,7 @@ def get_results(url_file):
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#dynamut_results_df = pd.DataFrame()
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for a in batch_soup.find_all('a', href=True, attrs = {'class':'btn btn-default btn-sm'}):
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print ("Found the URL:", a['href'])
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single_result_url = host + a['href']
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single_result_url = host_url + a['href']
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snp = re.search(r'([A-Z]+[0-9]+[A-Z]+$)', single_result_url).group(0)
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print(snp)
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print('\nGetting results from:', single_result_url)
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@ -68,24 +63,47 @@ def get_results(url_file):
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print('Result DF:', results_df, 'for URL:', line)
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#dynamut_results_df = dynamut_results_df.append(results_df)#!1 too many!:-)
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dynamut_results_out_df = dynamut_results_out_df.append(results_df)
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#print(dynamut_results_out_df)
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#============================
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# Writing results file: csv
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#============================
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dynamut_results_dir = outdir + '/dynamut_results'
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if not os.path.exists(dynamut_results_dir):
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print('\nCreating dir: dynamut_results within:', outdir )
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os.makedirs(dynamut_results_dir)
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print('\nWriting dynamut results df')
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print('\nResults File:'
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, '\nNo. of rows:', dynamut_results_out_df.shape[0]
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, '\nNo. of cols:', dynamut_results_out_df.shape[1])
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print(dynamut_results_out_df)
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dynamut_results_out_df.to_csv('/tmp/test_dynamut.csv', index = False)
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#dynamut_results_out_df.to_csv('/tmp/test_dynamut.csv', index = False)
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#%%
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# build out filename
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out_filename = dynamut_results_dir + '/dynamut_output_' + outfile_suffix + '.csv'
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dynamut_results_out_df.to_csv(out_filename, index = False)
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#%% EXAMPLE RUN
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# globals
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#homedir = os.path.expanduser('~')
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#my_host = 'http://biosig.unimelb.edu.au'
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#my_outdir = homedir + '/git/LSHTM_analysis/dynamut'
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#=============================================
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# example 1: multiple urls in a single file
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my_url_file_multiple = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_multiple.txt'
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print(my_url_file_multiple)
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get_results(my_url_file_multiple)
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#=============================================
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#my_url_file_multiple = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_multiple.txt'
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#print(my_url_file_multiple)
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#get_results(url_file = my_url_file_multiple
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# , host_url = my_host
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# , outdir = my_outdir
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# , outfile_suffix='multiple')
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#=============================================
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# example 2: single url in a file
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my_url_file_single = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_single.txt'
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print(my_url_file_multiple)
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get_results(my_url_file_single)
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#=============================================
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#my_url_file_single = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_single.txt'
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#print(my_url_file_multiple)
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#get_results(my_url_file_single
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# , host_url = my_host
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# , outdir = my_outdir
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# , outfile_suffix = 'single')
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#%%
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@ -31,7 +31,7 @@ def request_calculation(pdb_file
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#, out_url_file
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):
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"""
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Makes a POST request for a ligand affinity prediction.
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Makes a POST request for dynamut predictions.
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@param pdb_file: valid path to pdb structure
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@type string
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@ -100,12 +100,17 @@ indir = datadir + '/' + drug + '/input'
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outdir = datadir + '/' + drug + '/output'
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#outdir = homedir + '/git/LSHTM_analysis/dynamut' # for example
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my_pdb_file = homedir + '/git/Data/streptomycin/input/gid_complex.pdb'
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my_mutation_list = homedir + '/git/Data/streptomycin/output/snp_batches/50/snp_batch_00.txt'
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my_chain = 'A'
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my_batch = 1
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#my_outfile = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
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my_pdb_file = homedir + '/git/Data/streptomycin/input/gid_complex.pdb'
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# batch 1: 00.txt
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#my_mutation_list = homedir + '/git/Data/streptomycin/output/snp_batches/50/snp_batch_00.txt'
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#my_batch = 1
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# batch 2: 01.txt
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my_mutation_list = outdir + '/snp_batches/50/snp_batch_01.txt'
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my_batch = 2
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# %% call this function
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request_calculation (pdb_file = my_pdb_file
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, mutation_list = my_mutation_list
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