#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jun 18 11:32:28 2019

@author: tanushree
"""
############################################
# load libraries
import pandas as pd
import os
#############################################

#!#########################!
# REQUIREMNETS:
# Data_original/ must exist
# containing GWAS data
#!#########################!

#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(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

#=========================================================
#convert file to  dict of dicts
#=========================================================
#convert each row into a dict of dicts so that there are 20 aa and 5 keys within
#with your choice of column name that you have assigned to index as the "primary key". 
#using 'index' creates a dict of dicts
#using 'records' creates a list of dicts
my_aa_dict = my_aa.to_dict('index') #20, with 5 subkeys

#================================================
#dict of aa with their corresponding properties
#This is defined twice
#================================================
#7 categories: no overlap
qualities1 = { ('R', 'H', 'K'): 'Basic'
             , ('D', 'E'): 'Acidic'
             , ('N', 'Q'): 'Amidic'
             , ('G', 'A', 'V', 'L', 'I', 'P'): 'Hydrophobic'
             , ('S', 'T'): 'Hydroxylic'
             , ('F', 'W', 'Y'): 'Aromatic'
             , ('C', 'M'): 'Sulphur'
}

#9 categories: allowing for overlap
qualities2 = { ('R', 'H', 'K'): 'Basic'
             , ('D', 'E'): 'Acidc'
             , ('S', 'T', 'N', 'Q'): 'Polar'
             , ('V', 'I', 'L', 'M', 'F', 'Y', 'W'): 'Hydrophobic'
             , ('S', 'T', 'H', 'N', 'Q', 'E', 'D', 'K', 'R'): 'Hydrophilic'
             , ('S', 'G', 'A', 'P'): 'Small'
             , ('F', 'W', 'Y', 'H'): 'Aromatic'
             , ('V', 'I', 'L', 'M'): 'Aliphatic'
             , ('C', 'G', 'P'): 'Special'
}

qualities_taylor = { ('R', 'H', 'K'): 'Basic'
             , ('D', 'E'): 'Acidc'
             , ('S', 'T', 'N', 'Q', 'C', 'Y', 'W', 'H', 'K', 'R', 'D', 'E'): 'Polar'
             , ('V', 'I', 'L', 'M', 'F', 'Y', 'W', 'C', 'A', 'G', 'T', 'H'): 'Hydrophobic'
             #, ('S', 'T', 'H', 'N', 'Q', 'E', 'D', 'K', 'R'): 'Hydrophilic', #C, W, y MISSING FROM POLAR!
             , ('S', 'G', 'A', 'P', 'C', 'T', 'N', 'D', 'V'): 'Small' 
             , ('F', 'W', 'Y', 'H'): 'Aromatic'
             , ('V', 'I', 'L', 'M'): 'Aliphatic' #although M is not strictly in the circle!
             , ('C', 'G', 'P'): 'Special'
}

qualities_water = { ('D', 'E', 'N', 'P', 'Q', 'R', 'S'): 'hydrophilic'
                   , ('A', 'C', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'T', 'V', 'W', 'X', 'Y'): 'hydrophobic'
}

qualities_polarity = { ('D', 'E'): 'acidic'
                      , ('H', 'K', 'R'): 'basic'
                      , ('C', 'G', 'N', 'Q', 'S', 'T', 'Y'): 'neutral'
                      , ('A', 'F', 'I', 'L', 'M', 'P', 'V', 'W'): 'non-polar'    
}

#==============================================================================                
#adding amino acid properties to my dict of dicts                      
for k, v in my_aa_dict.items():
    #print (k,v)
    v['aa_prop1'] = str() #initialise keys 
    v['aa_prop2'] = list() #initialise keys (allows for overalpping properties)
    v['aa_taylor'] = list() #initialise keys (allows for overalpping properties)
    v['aa_prop_water'] = str() #initialise keys
    v['aa_prop_polarity'] = str() #initialise keys
    
    for group in qualities1:
        if v['one_letter_code'] in group:
            v['aa_prop1']+= qualities1[group] # += for str concat   

    for group in qualities2:
        if v['one_letter_code'] in group:
            v['aa_prop2'].append(qualities2[group]) # append to list
 
    for group in qualities_taylor:
        if v['one_letter_code'] in group:
            v['aa_taylor'].append(qualities_taylor[group]) # append to list           
            
    for group in qualities_water:
        if v['one_letter_code'] in group:
            v['aa_prop_water']+= qualities_water[group] # += for str concat          

    for group in qualities_polarity:
        if v['one_letter_code'] in group:
            v['aa_prop_polarity']+= qualities_polarity[group] # += for str concat 
             
#COMMENT:VOILA!!! my_aa_dict is now a dict of dicts containing all associated properties for each aa
#==============================================================================