From c8feba90bce21842ae7848ea0c18622e41fe0674 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Tue, 9 Feb 2021 20:16:27 +0000 Subject: [PATCH] added script to submit jobs --- dynamut/dynamut_reading_muts.py | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100755 dynamut/dynamut_reading_muts.py diff --git a/dynamut/dynamut_reading_muts.py b/dynamut/dynamut_reading_muts.py new file mode 100755 index 0000000..6f62ff9 --- /dev/null +++ b/dynamut/dynamut_reading_muts.py @@ -0,0 +1,36 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Wed Aug 19 14:33:51 2020 + +@author: tanu +""" + + +#%% load packages +import os,sys +import subprocess +import argparse +import requests +import re +import time +from bs4 import BeautifulSoup +import pandas as pd +import numpy as np +from pandas.api.types import is_string_dtype +from pandas.api.types import is_numeric_dtype +#%%============================================================================ +# read mutation file + +all_muts = pd.read_csv("/home/tanu/git/Data/streptomycin/output/snp_batches/snps_batch_00", header=None) +#https://gist.github.com/jrivero/1085501 +n = 20 +chunks = [all_muts[i:i+n] for i in range(0,all_muts.shape[0],n)] +#%% + +muts_list = all_muts[0].values.tolist() + +host_dynamut = 'http://biosig.unimelb.edu.au/dynamut' +mut_prediction = '/prediction' + +submit_url = host_dynamut + mut_prediction