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updated ref dict to inc aa_calcprop

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Tanushree Tunstall 2020-02-11 15:02:32 +00:00
parent d12ef0ef00
commit 0653a8c1e3
2 changed files with 16 additions and 5 deletions
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meta_data_analysis/__pycache__/reference_dict.cpython-37.pyc
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meta_data_analysis/reference_dict.py
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@ -13,20 +13,19 @@ import os
#!#########################! #!#########################!
# REQUIREMNETS: # REQUIREMNETS:
# Data_original/ must exist # Data/ must exist
# containing GWAS data # containing GWAS data
#!#########################! #!#########################!
#print(os.getcwd()) print(os.getcwd())
#homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde
#os.chdir(homedir + '/git/Data/pyrazinamide/input/original') os.chdir(homedir + '/git/Data/pyrazinamide/input/original')
print(os.getcwd()) print(os.getcwd())
#%% #%%
############# specify variables for input and output paths and filenames ############# specify variables for input and output paths and filenames
drug = 'pyrazinamide' drug = 'pyrazinamide'
#gene = 'pnca' #gene = 'pnca'
datadir = homedir + '/git/Data' datadir = homedir + '/git/Data'
basedir = datadir + '/' + drug + '/input' basedir = datadir + '/' + drug + '/input'
@ -100,6 +99,13 @@ qualities_polarity = { ('D', 'E'): 'acidic'
, ('A', 'F', 'I', 'L', 'M', 'P', 'V', 'W'): 'non-polar' , ('A', 'F', 'I', 'L', 'M', 'P', 'V', 'W'): 'non-polar'
} }
# almost same as the one above
aa_calcprop = { ('D', 'E'): 'neg'
, ('H', 'K', 'R'): 'pos'
, ('N', 'Q', 'S', 'T', 'Y'): 'polar'
, ('C', 'G', 'A', 'F', 'I', 'L', 'M', 'P', 'V', 'W'): 'non-polar'
}
#============================================================================== #==============================================================================
#adding amino acid properties to my dict of dicts #adding amino acid properties to my dict of dicts
for k, v in my_aa_dict.items(): for k, v in my_aa_dict.items():
@ -109,6 +115,7 @@ for k, v in my_aa_dict.items():
v['aa_taylor'] = 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_water'] = str() #initialise keys
v['aa_prop_polarity'] = str() #initialise keys v['aa_prop_polarity'] = str() #initialise keys
v['aa_calcprop'] = str() #initialise keys
for group in qualities1: for group in qualities1:
if v['one_letter_code'] in group: if v['one_letter_code'] in group:
@ -129,6 +136,10 @@ for k, v in my_aa_dict.items():
for group in qualities_polarity: for group in qualities_polarity:
if v['one_letter_code'] in group: if v['one_letter_code'] in group:
v['aa_prop_polarity']+= qualities_polarity[group] # += for str concat v['aa_prop_polarity']+= qualities_polarity[group] # += for str concat
for group in aa_calcprop:
if v['one_letter_code'] in group:
v['aa_calcprop']+= aa_calcprop[group] # += for str concat
#COMMENT:VOILA!!! my_aa_dict is now a dict of dicts containing all associated properties for each aa #COMMENT:VOILA!!! my_aa_dict is now a dict of dicts containing all associated properties for each aa
#============================================================================== #==============================================================================