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separated defs and calls and added a separate script to test examples

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Tanushree Tunstall 2021-02-12 14:15:55 +00:00
parent 6c458f8883
commit deb0aa8e58
13 changed files with 281 additions and 517 deletions
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dynamut/submit.py Executable file → Normal file
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@ -16,106 +16,72 @@ from bs4 import BeautifulSoup
import pandas as pd
from pandas.api.types import is_string_dtype
from pandas.api.types import is_numeric_dtype
#%% homedir
homedir = os.path.expanduser('~')
print('My homedir is:', homedir)
#%%
host = 'http://biosig.unimelb.edu.au'
prediction_url = f"{host}/dynamut/prediction_list"
print(prediction_url)
#%% example params
gene_name = 'gid'
drug = 'streptomycin'
datadir = homedir + '/git/Data'
indir = datadir + '/' + drug + '/input'
#outdir = datadir + '/' + drug + '/output'
outdir = homedir + '/git/LSHTM_analysis/dynamut' # for example
dynamut_temp_dir = outdir + '/dynamut_temp'
if not os.path.exists(dynamut_temp_dir):
print('Creating dynamut_temp in outdir', outdir )
os.makedirs(dynamut_temp_dir)
batch_no = 1
out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
#%% request calculation (no def)
with open("/home/tanu/git/Data/streptomycin/input/gid_complex.pdb", "rb") as pdb_file, open ("/home/tanu/git/LSHTM_analysis/dynamut/snp_test2.csv", "rb") as mutation_list:
files = {"wild": pdb_file
, "mutation_list": mutation_list}
body = {"chain": 'A'
, "email": 'tanushree.tunstall@lshtm.ac.uk'}
response = requests.post(prediction_url, files = files, data = body)
print(response.status_code)
if response.history:
print('PASS: valid mutation submitted. Fetching result url')
url_match = re.search('/dynamut/results_prediction/.+(?=")', response.text)
url = host + url_match.group()
print(url)
#===============
# writing file: result urls
#===============
out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
print('Writing output url file:', out_url_file)
myfile = open(out_url_file, 'a')
myfile.write(url)
myfile.close()
#%%
def request_calculation(pdb_file, mutation_list
#%%#####################################################################
def submit_dynamut(host_url
, pdb_file
, mutation_list
, chain
, my_email
, email_address
, prediction_url
, output_dir
, gene_name
, batch_no
, out_url_file):
, outfile_suffix
):
"""
Makes a POST request for a ligand affinity prediction.
Makes a POST request for dynamut predictions.
@param host_url: valid host url for submitting the job
@type string
@param pdb_file: valid path to pdb structure
@type string
@param mutation_list: list of mutations (1 per line) of the format: {WT}<POS>{Mut}
@type string
@param chain: single-letter(caps)
@type chr
@param prediction_url: dynamut url for prediction
@type string
@return txt file containing batch no. of snps processed
@param output_dir: output dir
@type string
@param outfile_suffix: outfile_suffix
@type string, default is batch no.
@param outfile_suffix: to append to outfile
@type string
@return writes a .txt file containing url for the snps processed with user provided suffix in filename
@type string
"""
with open(pdb_file, "rb") as pdb_file, open (mutation_list) as mutation_list:
with open(pdb_file, "rb") as pdb_file, open (mutation_list, "rb") as mutation_list:
files = {"wild": pdb_file
, "mutation_list": mutation_list}
body = {"chain": 'A'
, "email": 'tanushree.tunstall@lshtm.ac.uk'}
body = {"chain": chain
, "email": email_address}
response = requests.post(prediction_url, files = files, data = body)
print(response.status_code)
if response.history:
print('PASS: valid mutation submitted. Fetching result url')
print('\nPASS: valid submission. Fetching result url')
url_match = re.search('/dynamut/results_prediction/.+(?=")', response.text)
url = host + url_match.group()
print(url)
url = host_url + url_match.group()
print('\nURL for snp batch no ', str(outfile_suffix), ':', url)
#===============
# writing file: result urls
#===============
out_url_file = dynamut_temp_dir + '/dynamut_result_url_batch_' + str(batch_no) + '.txt'
print('Writing output url file:', out_url_file)
dynamut_temp_dir = output_dir + '/dynamut_temp' # creates a temp dir within output_dir
if not os.path.exists(dynamut_temp_dir):
print('\nCreating dynamut_temp in output_dir', output_dir )
os.makedirs(dynamut_temp_dir)
out_url_file = dynamut_temp_dir + '/dynamut_result_url_' + str(outfile_suffix) + '.txt'
print('\nWriting output url file:', out_url_file)
myfile = open(out_url_file, 'a')
myfile.write(url)
myfile.close()
#====================
# Submit first batch
#%%#####################################################################