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saving previous work from home pc

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This commit is contained in:
Tanushree Tunstall 2020-01-23 09:29:20 +00:00
parent cae9c550a4
commit be213cb7e9
3 changed files with 146 additions and 106 deletions
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25
meta_data_analysis/reference_dict.py
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@ -6,7 +6,7 @@ Created on Tue Jun 18 11:32:28 2019
@author: tanushree
"""
############################################
#load libraries
# load libraries
import pandas as pd
import os
#############################################
@ -17,14 +17,29 @@ import os
# containing GWAS data
#!#########################!
print(os.getcwd())
homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde
os.chdir(homedir + '/git/Data/input/original')
#print(os.getcwd())
#homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde
#os.chdir(homedir + '/git/Data/pyrazinamide/input/original')
print(os.getcwd())
#%%
############# specify variables for input and output paths and filenames
drug = 'pyrazinamide'
#gene = 'pnca'
datadir = homedir + '/git/Data'
basedir = datadir + '/' + drug + '/input'
# input
inpath = "/original"
in_filename = "/aa_codes.csv"
infile = basedir + inpath + in_filename
print(infile)
#==========
#read file
#==========
my_aa = pd.read_csv('aa_codes.csv') #20, 6
my_aa = pd.read_csv(infile) #20, 6
#assign the one_letter code as the row names so that it is easier to create a dict of dicts using index
#my_aa = pd.read_csv('aa_codes.csv', index_col = 0) #20, 6 #a way to it since it is the first column
my_aa = my_aa.set_index('three_letter_code_lower') #20, 5