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updated with def for get_results.py for dynamut

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Tanushree Tunstall 2021-02-11 19:21:26 +00:00
parent 2e047fd548
commit 1d8e6f0d75
1 changed files with 68 additions and 10 deletions
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78
dynamut/get_results_def.py
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@ -18,16 +18,74 @@ from pandas.api.types import is_string_dtype
from pandas.api.types import is_numeric_dtype from pandas.api.types import is_numeric_dtype
#%%============================================================================ #%%============================================================================
homedir = os.path.expanduser('~') homedir = os.path.expanduser('~')
print(homedir) #print(homedir)
host = 'http://biosig.unimelb.edu.au'
# Needed if things try to block the 'requests' user agent
#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"}
#%%
def get_results(url_file):
# initilialise empty df
dynamut_results_out_df = pd.DataFrame()
with open(url_file, 'r') as f:
for count, line in enumerate(f):
line = line.strip()
print('URL no.', count+1, '\n', line)
#batch_response = requests.get(line, headers=headers)
batch_response = requests.get(line)
batch_soup = BeautifulSoup(batch_response.text, features = 'html.parser')
# initilialise empty df
#dynamut_results_df = pd.DataFrame()
for a in batch_soup.find_all('a', href=True, attrs = {'class':'btn btn-default btn-sm'}):
print ("Found the URL:", a['href'])
single_result_url = host + a['href']
snp = re.search(r'([A-Z]+[0-9]+[A-Z]+$)', single_result_url).group(0)
print(snp)
print('\nGetting results from:', single_result_url)
result_response = requests.get(single_result_url)
if result_response.status_code == 200:
print('\nFetching results for SNP:', snp)
# extract results using the html parser
soup = BeautifulSoup(result_response.text, features = 'html.parser')
#web_result_raw = soup.find(id = 'predictions').get_text()
ddg_dynamut = soup.find(id = 'ddg_dynamut').get_text()
ddg_encom = soup.find(id = 'ddg_encom').get_text()
ddg_mcsm = soup.find(id = 'ddg_mcsm').get_text()
ddg_sdm = soup.find(id = 'ddg_sdm').get_text()
ddg_duet = soup.find(id = 'ddg_duet').get_text()
dds_encom = soup.find(id = 'dds_encom').get_text()
param_dict = {"mutationinformation" : snp
, "ddg_dynamut" : ddg_dynamut
, "ddg_encom" : ddg_encom
, "ddg_mcsm" : ddg_mcsm
, "ddg_sdm" : ddg_sdm
, "ddg_duet" : ddg_duet
, "dds_encom" : dds_encom
}
results_df = pd.DataFrame.from_dict(param_dict, orient = "index").T
print('Result DF:', results_df, 'for URL:', line)
#dynamut_results_df = dynamut_results_df.append(results_df)#!1 too many!:-)
dynamut_results_out_df = dynamut_results_out_df.append(results_df)
#print(dynamut_results_out_df)
print('\nWriting dynamut results df')
print('\nResults File:'
, '\nNo. of rows:', dynamut_results_out_df.shape[0]
, '\nNo. of cols:', dynamut_results_out_df.shape[1])
print(dynamut_results_out_df)
dynamut_results_out_df.to_csv('/tmp/test_dynamut.csv', index = False)
my_mutation_list = homedir + '/git/LSHTM_analysis/dynamut/test_input/snp_test2.csv' #%%
# example 1: multiple urls in a single file
my_url_file_multiple = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_multiple.txt'
print(my_url_file_multiple)
get_results(my_url_file_multiple)
text_file = open(my_mutation_list, 'r') # example 2: single url in a file
lines = text_file .read().split('\n') my_url_file_single = homedir + '/git/LSHTM_analysis/dynamut/dynamut_temp/dynamut_result_url_batch_single.txt'
print (lines) print(my_url_file_multiple)
print(len(lines)) get_results(my_url_file_single)
#%%
def get_results(url_file
, mutation_list)