added aa_prop.py and add_aa_prop.py to add aa properties for wt and mutant in a given file containing one letter code wt and mut cols as csv
This commit is contained in:
parent
58b5b63595
commit
0881181f4b
2 changed files with 304 additions and 0 deletions
113
scripts/aa_prop.py
Normal file
113
scripts/aa_prop.py
Normal file
|
|
@ -0,0 +1,113 @@
|
||||||
|
#!/usr/bin/env python3
|
||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
'''
|
||||||
|
Created on Mon June 14 2021
|
||||||
|
|
||||||
|
@author: tanu
|
||||||
|
'''
|
||||||
|
# FIXME: import dirs.py to get the basic dir paths available
|
||||||
|
#=======================================================================
|
||||||
|
# TASK
|
||||||
|
|
||||||
|
# Input:
|
||||||
|
|
||||||
|
# Output:
|
||||||
|
#=======================================================================
|
||||||
|
#%% load libraries
|
||||||
|
import os, sys
|
||||||
|
import pandas as pd
|
||||||
|
#import numpy as np
|
||||||
|
#from varname import nameof
|
||||||
|
import argparse
|
||||||
|
|
||||||
|
DEBUG = False
|
||||||
|
#=======================================================================
|
||||||
|
#%% specify input and curr dir
|
||||||
|
homedir = os.path.expanduser('~')
|
||||||
|
|
||||||
|
# set working dir
|
||||||
|
os.getcwd()
|
||||||
|
os.chdir(homedir + '/git/LSHTM_analysis/scripts')
|
||||||
|
os.getcwd()
|
||||||
|
|
||||||
|
from reference_dict import oneletter_aa_dict
|
||||||
|
#=======================================================================
|
||||||
|
#%%
|
||||||
|
def get_aa_prop(df, col1 = 'aap1', col2 = 'aap2', col3 = 'aap_taylor', col4 = 'aap_kd', col5 = 'aap_polarity', col6 = 'aap_calcprop'):
|
||||||
|
|
||||||
|
"""Add amino acid properties for wt and mutant residues
|
||||||
|
|
||||||
|
@df: df containing one letter aa code for wt and mutant respectively
|
||||||
|
@type: pandas df
|
||||||
|
|
||||||
|
@col1: column adding 7 aa categories (no overlap; acidic, basic, amidic, hydrophobic, hydroxylic, aromatic, sulphur)
|
||||||
|
@type: str
|
||||||
|
|
||||||
|
@col2: column adding 9 aa categories (overlap; acidic, basic, polar, hydrophobic, hydrophilic, small, aromatic, aliphatic, special)
|
||||||
|
@type: str
|
||||||
|
|
||||||
|
@col3: column adding 8 aa categories (overlap; acidic, basic, polar, hydrophobic, small, aromatic, aliphatic, special)
|
||||||
|
@type: str
|
||||||
|
|
||||||
|
@col4: column adding 3 aa categories (no overlap, hydrophobic, neutral and hydrophilic according to KD scale)
|
||||||
|
@type: str
|
||||||
|
|
||||||
|
@col5: column adding 4 aa categories (no overlap, acidic, basic, neutral, non-polar)
|
||||||
|
@type: str
|
||||||
|
|
||||||
|
@col6: column adding 4 aa categories (neg, pos, polar, non-polar)
|
||||||
|
@type: str
|
||||||
|
|
||||||
|
returns df: with 6 added columns. If column names clash, the function column
|
||||||
|
name will override original column
|
||||||
|
@rtype: pandas df
|
||||||
|
"""
|
||||||
|
|
||||||
|
lookup_dict_p1 = dict()
|
||||||
|
lookup_dict_p2 = dict()
|
||||||
|
|
||||||
|
lookup_dict_taylor = dict()
|
||||||
|
lookup_dict_kd = dict()
|
||||||
|
|
||||||
|
lookup_dict_polarity = dict()
|
||||||
|
lookup_dict_calcprop = dict()
|
||||||
|
|
||||||
|
for k, v in oneletter_aa_dict.items():
|
||||||
|
|
||||||
|
lookup_dict_p1[k] = v['aa_prop1']
|
||||||
|
|
||||||
|
lookup_dict_p2[k] = v['aa_prop2']
|
||||||
|
|
||||||
|
lookup_dict_taylor[k] = v['aa_taylor']
|
||||||
|
|
||||||
|
lookup_dict_kd[k] = v['aa_prop_water']
|
||||||
|
|
||||||
|
lookup_dict_polarity[k] = v['aa_prop_polarity']
|
||||||
|
|
||||||
|
lookup_dict_calcprop[k] = v['aa_calcprop']
|
||||||
|
|
||||||
|
#if DEBUG:
|
||||||
|
# print('Key:', k, 'value:', v
|
||||||
|
# , '\n============================================================'
|
||||||
|
# , '\nlook up dict:\n')
|
||||||
|
|
||||||
|
df['wt_aap1'] = df['wild_type'].map(lookup_dict_p1)
|
||||||
|
df['mut_aap1'] = df['mutant_type'].map(lookup_dict_p1)
|
||||||
|
|
||||||
|
df['wt_aap2'] = df['wild_type'].map(lookup_dict_p2)
|
||||||
|
df['mut_aap2'] = df['mutant_type'].map(lookup_dict_p2)
|
||||||
|
|
||||||
|
df['wt_aap_taylor'] = df['wild_type'].map(lookup_dict_taylor)
|
||||||
|
df['mut_aap_taylor'] = df['mutant_type'].map(lookup_dict_taylor)
|
||||||
|
|
||||||
|
df['wt_aap_kd'] = df['wild_type'].map(lookup_dict_kd)
|
||||||
|
df['mut_aap_kd'] = df['mutant_type'].map(lookup_dict_kd)
|
||||||
|
|
||||||
|
df['wt_aap_polarity'] = df['wild_type'].map(lookup_dict_polarity)
|
||||||
|
df['mut_aap_polarity'] = df['mutant_type'].map(lookup_dict_polarity)
|
||||||
|
|
||||||
|
df['wt_aa_calcprop'] = df['wild_type'].map(lookup_dict_calcprop)
|
||||||
|
df['mut_aa_calcprop'] = df['mutant_type'].map(lookup_dict_calcprop)
|
||||||
|
|
||||||
|
return df
|
||||||
|
#========================================
|
||||||
191
scripts/add_aa_prop.py
Normal file
191
scripts/add_aa_prop.py
Normal file
|
|
@ -0,0 +1,191 @@
|
||||||
|
#!/usr/bin/env python3
|
||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
'''
|
||||||
|
Created on Tue Aug 6 12:56:03 2019
|
||||||
|
|
||||||
|
@author: tanu
|
||||||
|
'''
|
||||||
|
# FIXME: import dirs.py to get the basic dir paths available
|
||||||
|
#=======================================================================
|
||||||
|
# TASK:
|
||||||
|
#
|
||||||
|
|
||||||
|
# Input:
|
||||||
|
|
||||||
|
# Output:
|
||||||
|
#=======================================================================
|
||||||
|
#%% load libraries
|
||||||
|
import os, sys
|
||||||
|
import pandas as pd
|
||||||
|
#import numpy as np
|
||||||
|
#from varname import nameof
|
||||||
|
import argparse
|
||||||
|
#=======================================================================
|
||||||
|
#%% specify input and curr dir
|
||||||
|
homedir = os.path.expanduser('~')
|
||||||
|
|
||||||
|
# set working dir
|
||||||
|
os.getcwd()
|
||||||
|
os.chdir(homedir + '/git/LSHTM_analysis/scripts')
|
||||||
|
os.getcwd()
|
||||||
|
|
||||||
|
from aa_prop import get_aa_prop
|
||||||
|
#=======================================================================
|
||||||
|
#%% command line args
|
||||||
|
arg_parser = argparse.ArgumentParser()
|
||||||
|
arg_parser.add_argument('-d', '--drug', help='drug name', default = None)
|
||||||
|
arg_parser.add_argument('-g', '--gene', help='gene name', default = None)
|
||||||
|
|
||||||
|
arg_parser.add_argument('--datadir', help = 'Data Directory. By default, it assmumes homedir + git/Data')
|
||||||
|
arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
|
||||||
|
arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
|
||||||
|
|
||||||
|
arg_parser.add_argument('--debug', action ='store_true', help = 'Debug Mode') # not used atm
|
||||||
|
|
||||||
|
args = arg_parser.parse_args()
|
||||||
|
#%% variable assignment: input and output
|
||||||
|
drug = args.drug
|
||||||
|
gene = args.gene
|
||||||
|
datadir = args.datadir
|
||||||
|
indir = args.input_dir
|
||||||
|
outdir = args.output_dir
|
||||||
|
|
||||||
|
#%%=======================================================================
|
||||||
|
#==============
|
||||||
|
# directories
|
||||||
|
#==============
|
||||||
|
if not datadir:
|
||||||
|
datadir = homedir + '/' + 'git/Data'
|
||||||
|
|
||||||
|
if not indir:
|
||||||
|
indir = datadir + '/' + drug + '/input'
|
||||||
|
|
||||||
|
if not outdir:
|
||||||
|
outdir = datadir + '/' + drug + '/output'
|
||||||
|
|
||||||
|
#=======
|
||||||
|
# input
|
||||||
|
#=======
|
||||||
|
#in_filename = 'merged_df3.csv'
|
||||||
|
#in_filename = gene.lower() + '_complex_mcsm_norm.csv'
|
||||||
|
in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SRY.csv' # gid
|
||||||
|
infile_mcsm = outdir + '/' + in_filename_mcsm
|
||||||
|
print('Input file: ', infile_mcsm
|
||||||
|
, '\n============================================================')
|
||||||
|
|
||||||
|
#=======
|
||||||
|
# output
|
||||||
|
#=======
|
||||||
|
out_filename_aaps = gene.lower() + '_mcsm_aaps.txt'
|
||||||
|
outfile_aaps = outdir + '/' + out_filename_aaps
|
||||||
|
print('Output file: ', outfile_aaps
|
||||||
|
, '\n============================================================')
|
||||||
|
|
||||||
|
#%% end of variable assignment for input and output files
|
||||||
|
#=======================================================================
|
||||||
|
#%% Read input files
|
||||||
|
print('Reading input file (merged file):', infile_mcsm)
|
||||||
|
|
||||||
|
comb_df = pd.read_csv(infile_mcsm, sep = ',')
|
||||||
|
|
||||||
|
print('Input filename: ', in_filename_mcsm
|
||||||
|
, '\nPath :', outdir
|
||||||
|
, '\nNo. of rows: ', len(comb_df)
|
||||||
|
, '\nNo. of cols: ', len(comb_df.columns)
|
||||||
|
, '\n============================================================')
|
||||||
|
|
||||||
|
# column names
|
||||||
|
list(comb_df.columns)
|
||||||
|
|
||||||
|
#%% sanity check
|
||||||
|
nrows_df = len(comb_df)
|
||||||
|
ncols_add = 12
|
||||||
|
expected_cols = len(comb_df.columns) + ncols_add
|
||||||
|
print('\nAdding aa properties for wt and mutant: ', ncols_add, ' columns in total'
|
||||||
|
, '\n===============================================================')
|
||||||
|
|
||||||
|
#%% call get_aa_prop():
|
||||||
|
get_aa_prop(df = comb_df)
|
||||||
|
|
||||||
|
#%% check dim of df
|
||||||
|
if len(comb_df) == nrows_df and len(comb_df.columns) == expected_cols:
|
||||||
|
print('Checking dim of df: '
|
||||||
|
, '\nPASS: df dim match'
|
||||||
|
, '\nno.of rows: ', len(comb_df)
|
||||||
|
, '\nno. of cols: ', len(comb_df.columns))
|
||||||
|
else:
|
||||||
|
print('\FAIL: dim mismatch'
|
||||||
|
, 'Expected rows: ', nrows_df
|
||||||
|
, '\Got: ', len(comb_df)
|
||||||
|
, '\nExpected cols: ', expected_cols
|
||||||
|
, '\nGot: ', len(comb_df.columns))
|
||||||
|
sys.exit('Aborting')
|
||||||
|
#%% summary output
|
||||||
|
sys.stdout = open(outfile_aaps, 'w')
|
||||||
|
|
||||||
|
print('################################################'
|
||||||
|
, '\n aa properties: ', gene
|
||||||
|
, '\n################################################')
|
||||||
|
|
||||||
|
print('\n-------------------'
|
||||||
|
, '\nWild-type: aap 1'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['wt_aap1'].value_counts()
|
||||||
|
, '\n-------------------'
|
||||||
|
, '\nmutant-type: aap 1'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['mut_aap1'].value_counts()
|
||||||
|
, '\n===================================================')
|
||||||
|
|
||||||
|
print('\n-------------------'
|
||||||
|
, '\nWild-type: aap 2'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['wt_aap2'].value_counts()
|
||||||
|
, '\n-------------------'
|
||||||
|
, '\nmutant-type: aap 2'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['mut_aap2'].value_counts()
|
||||||
|
, '\n===================================================')
|
||||||
|
|
||||||
|
print('\n-------------------'
|
||||||
|
, '\nWild-type: aap taylor'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['wt_aap_taylor'].value_counts()
|
||||||
|
, '\n-------------------'
|
||||||
|
, '\nmutant-type: taylor'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['mut_aap_taylor'].value_counts()
|
||||||
|
, '\n===================================================')
|
||||||
|
|
||||||
|
print('\n-------------------'
|
||||||
|
, '\nWild-type: aap water/kd'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['wt_aap_kd'].value_counts()
|
||||||
|
, '\n-------------------'
|
||||||
|
, '\nmutant-type: water/kd'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['mut_aap_kd'].value_counts()
|
||||||
|
, '\n===================================================')
|
||||||
|
|
||||||
|
print('\n-------------------'
|
||||||
|
, '\nWild-type: aap polarity'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['wt_aap_polarity'].value_counts()
|
||||||
|
, '\n-------------------'
|
||||||
|
, '\nmutant-type: polarity'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['mut_aap_polarity'].value_counts()
|
||||||
|
, '\n===================================================')
|
||||||
|
|
||||||
|
print('\n-------------------'
|
||||||
|
, '\nWild-type: aa calcprop'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['wt_aa_calcprop'].value_counts()
|
||||||
|
, '\n-------------------'
|
||||||
|
, '\nmutant-type: aa calcprop'
|
||||||
|
, '\n-------------------\n'
|
||||||
|
, comb_df['mut_aa_calcprop'].value_counts()
|
||||||
|
, '\n===================================================')
|
||||||
|
|
||||||
|
#%% end of script
|
||||||
|
#=======================================================================
|
||||||
Loading…
Add table
Add a link
Reference in a new issue