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saving work for mcsm_na

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This commit is contained in:
Tanushree Tunstall 2021-02-15 12:22:19 +00:00
parent 322979406c
commit 7a74fecbda
4 changed files with 13 additions and 59 deletions
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2
dynamut/run_results.py
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@ -23,8 +23,10 @@ datadir = homedir + '/git/Data'
indir = datadir + '/' + drug + '/input'
outdir = datadir + '/' + drug + '/output'
# batch 1: 00.txt
my_url_file = outdir + '/dynamut_temp/dynamut_result_url_gid_b1.txt'
my_suffix = 'gid_b1'
#==========================
# CALL: get_results()
# Data: gid+streptomycin

2
mcsm_na/examples.py
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@ -9,7 +9,7 @@ import os
homedir = os.path.expanduser('~')
os.chdir (homedir + '/git/LSHTM_analysis/mcsm_na')
from submit_mcsm_na import *
from get_results import *
from get_results_mcsm_na import *
#%%#####################################################################
#EXAMPLE RUN for different stages
#=====================

53
mcsm_na/get_results.py
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@ -1,53 +0,0 @@
#!/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
from pandas.api.types import is_string_dtype
from pandas.api.types import is_numeric_dtype
#%%#####################################################################
def get_results(url_file, host_url, output_dir, outfile_suffix):
# initilialise empty df
#mcsm_na_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)
#============================
# Writing results file: csv
#============================
mcsm_na_results_dir = output_dir + '/mcsm_na_results'
if not os.path.exists(mcsm_na_results_dir):
print('\nCreating dir: mcsm_na_results within:', output_dir )
os.makedirs(mcsm_na_results_dir)
# TODO: add as a cmd option
# Download .tar.gz file
prediction_number = re.search(r'([0-9]+\.[0-9]+$)', line).group(0)
print('CHECK prediction no:', prediction_number)
txt_url = f"{host_url}/mcsm_na/static/results/" + prediction_number + '.txt'
print('CHECK txt url:', txt_url)
out_filename = mcsm_na_results_dir + '/' + outfile_suffix + '_output_' + prediction_number + '.txt'
response_txt = requests.get(txt_url, stream = True)
if response_txt.status_code == 200:
print('\nDownloading .txt:', txt_url
, '\n\nSaving file as:', out_filename)
with open(out_filename, 'wb') as f:
f.write(response_txt.raw.read())
#%%#####################################################################

15
mcsm_na/run_submit.py
View file

@ -8,7 +8,7 @@ Created on Fri Feb 12 12:15:26 2021
#%% load packages
import os
homedir = os.path.expanduser('~')
os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
os.chdir (homedir + '/git/LSHTM_analysis/mcsm_na')
from submit_mcsm_na import *
########################################################################
# variables
@ -26,10 +26,15 @@ outdir = datadir + '/' + drug + '/output'
my_nuc_type = 'RNA'
my_pdb_file = indir + '/gid_complex.pdb'
# batch 1: 00.txt
my_mutation_list = outdir + '/snp_batches/20/snp_batch_00.txt'
my_suffix = 'gid_b1'
#RAN: 11 Feb, ~17:37
# batch 1: 00.txt: # RAN: 11 Feb, ~17:37, RETRIEVED: 15 Feb~ 12:18
#my_mutation_list = outdir + '/snp_batches/20/snp_batch_00.txt'
#my_suffix = 'gid_b1'
# batch 2: 01.txt
my_mutation_list = outdir + '/snp_batches/20/snp_batch_01.txt'
my_suffix = 'gid_b2'
# RAN: 15 Feb: 12:18
#==========================
# CALL: submit_mcsm_na()