tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

dynamut scripts and minor change dir for rd_df.py

Browse source
This commit is contained in:
Tanushree Tunstall 2021-02-10 15:40:33 +00:00
parent 0fd3e75ab0
commit fad1526ce5
3 changed files with 8 additions and 10 deletions
Download patch file Download diff file Expand all files Collapse all files

12
dynamut/get_results.py
View file

@ -5,8 +5,6 @@ Created on Wed Aug 19 14:33:51 2020
@author: tanu @author: tanu
""" """
#%% load packages #%% load packages
import os,sys import os,sys
import subprocess import subprocess
@ -20,15 +18,15 @@ 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 #streptomycin/gid_complex.pdb
host_dynamut = 'http://biosig.unimelb.edu.au/dynamut' host = 'http://biosig.unimelb.edu.au/dynamut'
pred_dynamut_batch = '/results_prediction/161287964015' pred_dynamut_batch = '/results_prediction/161287964015'
result_id = re.search( r"([0-9]+)$", pred_dynamut).group(0) result_id = re.search( r"([0-9]+)$", pred_dynamut).group(0)
batch_result_url = host_dynamut + pred_dynamut_batch batch_result_url = host + pred_dynamut_batch
mut = 'S2C' mut = 'S2C'
single_url = host_dynamut + '/single_results/' + str(result_id) single_url = host + '/single_results/' + str(result_id)
single_result_url = host_dynamut + '/single_results/' + str(result_id) + '/' + mut single_result_url = host + '/single_results/' + str(result_id) + '/' + mut
print(single_result_url) print(single_result_url)
#%%============================================================================ #%%============================================================================
@ -62,7 +60,7 @@ print(results_df)
#%% for loop #%% for loop
single_url = host_dynamut + '/single_results/' + str(result_id) single_url = host + '/single_results/' + str(result_id)
muts = ["S2C", "S2F"] muts = ["S2C", "S2F"]

4
dynamut/reading_muts.py
View file

@ -30,7 +30,7 @@ chunks = [all_muts[i:i+n] for i in range(0,all_muts.shape[0],n)]
muts_list = all_muts[0].values.tolist() muts_list = all_muts[0].values.tolist()
host_dynamut = 'http://biosig.unimelb.edu.au/dynamut' host = 'http://biosig.unimelb.edu.au/dynamut'
mut_prediction = '/prediction' mut_prediction = '/prediction'
submit_url = host_dynamut + mut_prediction submit_url = host + mut_prediction

2
scripts/rd_df.py
View file

@ -26,7 +26,7 @@ homedir = os.path.expanduser('~')
# set working dir # set working dir
os.getcwd() os.getcwd()
os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis') os.chdir(homedir + '/git/LSHTM_analysis/scripts')
os.getcwd() os.getcwd()
#======================================================================= #=======================================================================
#%% command line args #%% command line args