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refactoring or_kin script minor changes only

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Tanushree Tunstall 2020-07-10 12:38:42 +01:00
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scripts/or_kinship_link.py Executable file
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Jun 10 11:13:49 2020
@author: tanu
"""
#=======================================================================
#%% useful links
#https://chrisalbon.com/python/data_wrangling/pandas_join_merge_dataframe/
#https://kanoki.org/2019/11/12/how-to-use-regex-in-pandas/
#https://stackoverflow.com/questions/40348541/pandas-diff-with-string
#=======================================================================
#%% specify dirs
import os, sys
import pandas as pd
import numpy as np
import re
import argparse
homedir = os.path.expanduser('~')
os.chdir(homedir + '/git/LSHTM_analysis/scripts')
# local import
from find_missense import find_missense
#=======================================================================
#%% 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 (case sensitive)', 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')
# FIXME: remove defaults
arg_parser.add_argument('-s', '--start_coord', help = 'start of coding region (cds) of gene', default = 2288681) # pnca cds
arg_parser.add_argument('-e', '--end_coord', help = 'end of coding region (cds) of gene', default = 2289241) # pnca cds
arg_parser.add_argument('--debug', action ='store_true', help = 'Debug Mode')
args = arg_parser.parse_args()
#=======================================================================
#%% variables
#gene = 'pncA'
#drug = 'pyrazinamide'
#start_cds = 2288681
#end_cds = 2289241
# cmd variables
gene = args.gene
drug = args.drug
gene_match = gene + '_p.'
datadir = args.datadir
indir = args.input_dir
outdir = args.output_dir
start_cds = args.start_coord
end_cds = args.end_coord
#=======================================================================
#%% input and output dirs and files
#==============
# directories
#==============
if not datadir:
datadir = homedir + '/' + 'git/Data'
if not indir:
indir = datadir + '/' + drug + '/input'
if not outdir:
outdir = datadir + '/' + drug + '/output'
#=======
# input
#=======
info_filename = 'snp_info.txt'
snp_info = datadir + '/' + info_filename
print('Info file: ', snp_info
, '\n============================================================')
#gene_info_filename = 'ns'+ gene.lower()+ '_snp_info.txt' # without headers
gene_info_filename = 'ns'+ gene.lower()+ '_snp_info.csv'
gene_info = indir + '/' + gene_info_filename
print('gene info file: ', gene_info
, '\n============================================================')
in_filename_or = 'ns'+ gene.lower()+ '_assoc.txt'
gene_or = indir + '/' + in_filename_or
print('gene OR file: ', gene_or
, '\n============================================================')
#=======
# output
#=======
gene_or_filename = gene.lower() + '_af_or_kinship.csv' # other one is called AFandOR
outfile_or_kin = outdir + '/' + gene_or_filename
print('Output file: ', outfile_or_kin
, '\n============================================================')
#%% read files: preformatted using bash
# or file: '...assoc.txt'
# FIXME: call bash script from here
or_df = pd.read_csv(gene_or, sep = '\t', header = 0, index_col = False) # 182, 12 (without filtering for missense muts, it was 212 i.e we 30 muts weren't missense)
or_df.head()
or_df.columns
#%% snp_info file: master and gene specific ones
# gene info
#info_df2 = pd.read_csv('nssnp_info_pnca.txt', sep = '\t', header = 0) #303, 10
info_df2 = pd.read_csv(gene_info, sep = ',', header = 0) #303, 10
mis_mut_cover = (info_df2['chromosome_number'].nunique()/info_df2['chromosome_number'].count()) * 100
print('*****RESULT*****'
, '\nPercentage of missense mut in pncA:', mis_mut_cover
, '\n*****RESULT*****') #65.7%
# large file
#info_df = pd.read_csv('snp_info.txt', sep = '\t', header = None) #12010
info_df = pd.read_csv(snp_info, sep = '\t') #12010
info_df.columns
#info_df.columns = ['chromosome_number', 'ref_allele', 'alt_allele', 'snp_info'] #12009, 4
info_df['chromosome_number'].nunique() #10257
mut_cover = (info_df['chromosome_number'].nunique()/info_df['chromosome_number'].count()) * 100
print('*****RESULT*****'
,'\nPercentage of mutations in pncA:', mut_cover
, '\n*****RESULT*****') #85.4%
# extract unique chr position numbers
genomic_pos = info_df['chromosome_number'].unique()
genomic_pos_df = pd.DataFrame(genomic_pos, columns = ['chr_pos'])
genomic_pos_df.dtypes
genomic_pos_min = info_df['chromosome_number'].min()
genomic_pos_max = info_df['chromosome_number'].max()
# genomic coord for pnca coding region
cds_len = (end_cds-start_cds) + 1
pred_prot_len = (cds_len/3) - 1
# mindblowing: difference b/w bitwise (&) and 'and'
# DO NOT want &: is this bit set to '1' in both variables? Is this what you want?
#if (genomic_pos_min <= start_cds) & (genomic_pos_max >= end_cds):
print('*****RESULT*****'
, '\nlength of coding region:', cds_len, 'bp'
, '\npredicted protein length:', pred_prot_len, 'aa'
, '\n*****RESULT*****')
if genomic_pos_min <= start_cds and genomic_pos_max >= end_cds:
print ('PASS: coding region for gene included in snp_info.txt')
else:
sys.exit('FAIL: coding region for gene not included in info file snp_info.txt')
#%% Extracting ref allele and alt allele as single letters
# info_df has some of these params as more than a single letter, which means that
# when you try to merge ONLY using chromosome_number, then it messes up... and is WRONG.
# Hence the merge needs to be performed on a unique set of attributes which in our case
# would be chromosome_number, ref_allele and alt_allele
orig_len = len(or_df.columns)
#find_missense(or_df, 'ref_allele1', 'alt_allele0')
# adds columns to df passed
find_missense(or_df, ref_allele_column = 'ref_allele1', alt_allele_column = 'alt_allele0')
ncols_add = 4
if len(or_df.columns) == orig_len + ncols_add:
print('PASS: Succesfuly extracted ref and alt alleles for missense muts')
else:
print('FAIL: No. of cols mismatch'
,'\noriginal length:', orig_len
, '\nExpected no. of cols:', orig_len + ncols_add
, '\nGot no. of cols:', len(or_df.columns)
, '\nCheck hardcoded value of ncols_add?')
sys.exit()
del(orig_len, ncols_add)
#%% TRY MERGE
# check dtypes
or_df.dtypes
info_df.dtypes
#or_df.info()
# pandas documentation where it mentions: "Pandas uses the object dtype for storing strings"
# check how many unique chr_num in info_df are in or_df
genomic_pos_df['chr_pos'].isin(or_df['chromosome_number']).sum() #144
# check how many chr_num in or_df are in info_df: should be ALL of them
or_df['chromosome_number'].isin(genomic_pos_df['chr_pos']).sum() #182
# sanity check 2
if or_df['chromosome_number'].isin(genomic_pos_df['chr_pos']).sum() == len(or_df):
print('PASS: all genomic locs in or_df have meta datain info.txt')
else:
sys.exit('FAIL: some genomic locs or_df chr number DO NOT have meta data in snp_info.txt')
#%% Perform merge
#my_join = 'inner'
#my_join = 'outer'
my_join = 'left'
#my_join = 'right'
#dfm1 = pd.merge(or_df, info_df, on ='chromosome_number', how = my_join, indicator = True) # not unique!
dfm1 = pd.merge(or_df, info_df, on = ['chromosome_number', 'ref_allele', 'alt_allele'], how = my_join, indicator = True)
dfm1['_merge'].value_counts()
# count no. of missense mutations ONLY
dfm1.snp_info.str.count(r'(missense.*)').sum()
dfm2 = pd.merge(or_df, info_df2, on = ['chromosome_number', 'ref_allele', 'alt_allele'], how = my_join, indicator = True)
dfm2['_merge'].value_counts()
print(or_df.columns, info_df2.columns)
# count no. of nan
print('No. of NA in dfm2:', dfm2['mut_type'].isna().sum())
# drop nan
#dfm2_mis = dfm2[dfm2['mut_type'].notnull()]
#%% sanity check
# count no. of missense muts
if len(dfm1) - dfm1.snp_info.str.count(r'(missense.*)').sum() == dfm2['mut_type'].isna().sum():
print('PASSED: numbers cross checked'
, '\nTotal no. of missense mutations:', dfm1.snp_info.str.count(r'(missense.*)').sum()
, '\nNo. of mutations falsely assumed to be missense:', len(dfm1) - dfm1.snp_info.str.count(r'(missense.*)').sum())
# two ways to filter to get only missense muts
test = dfm1[dfm1['snp_info'].str.count('missense.*')>0]
dfm1_mis = dfm1[dfm1['snp_info'].str.match('(missense.*)') == True]
test.equals(dfm1_mis)
# drop nan from dfm2
dfm2_mis = dfm2[dfm2['mut_type'].notnull()]
if dfm1_mis[['chromosome_number', 'ref_allele', 'alt_allele']].equals(dfm2_mis[['chromosome_number', 'ref_allele', 'alt_allele']]):
print('PASS: Further cross checks successful')
else:
sys.exit('FAIL: Second cross check unsuccessfull!')
#%% extract mut info into three cols
orig_len = len(dfm2_mis.columns)
print('Dim of df to add cols to:', dfm2_mis.shape)
# column names already present, wrap this in a if and perform sanity check
ncols_add = 0
if not 'wild_type' in dfm2_mis.columns:
print('Extracting and adding column: wild_type'
, '\n======================================')
dfm2_mis['wild_type'] = dfm2_mis['mut_info'].str.extract('(\w{1})>')
ncols_add+=1
if not 'position' in dfm2_mis.columns:
print('Extracting and adding column: position'
, '\n======================================')
dfm2_mis['position'] = dfm2_mis['mut_info'].str.extract('(\d+)')
ncols_add+=1
if not 'mutant_type' in dfm2_mis.columns:
print('Extracting and adding column: mutant_type'
, '\n======================================')
dfm2_mis['mutant_type'] = dfm2_mis['mut_info'].str.extract('>\d+(\w{1})')
ncols_add+=1
if not 'mutationinformation' in dfm2_mis.columns:
print('combining to create column: mutationinformation'
, '\n======================================')
dfm2_mis['mutationinformation'] = dfm2_mis['wild_type'] + dfm2_mis['position'] + dfm2_mis['mutant_type']
ncols_add+=1
print('No. of cols added:', ncols_add)
if len(dfm2_mis.columns) == orig_len + ncols_add:
print('PASS: mcsm style muts present in df'
, '\n======================================')
else:
print('FAIL: No. of cols mismatch'
,'\nOriginal length:', orig_len
, '\nExpected no. of cols:', orig_len + ncols_add
, '\nGot:', len(dfm2_mis.columns))
sys.exit()
del(ncols_add)
#%% formatting data for output
print('no of cols pre-formatting data:', len(dfm2_mis.columns)
, '\n======================================')
#1) Add column: OR for kinship calculated from beta coeff
print('converting beta coeff to OR by exponent function\n:'
, dfm2_mis['beta'].head()
, '\n======================================')
dfm2_mis['or_kin'] = np.exp(dfm2_mis['beta'])
print(dfm2_mis['or_kin'].head())
print('No. of cols after adidng OR kinship:', len(dfm2_mis.columns))
#2) rename af column
dfm2_mis.rename(columns = {'af': 'af_kin'
, 'beta': 'beta_kin'
, 'p_wald': 'pwald_kin'
, 'se': 'se_kin', 'logl_H1': 'logl_H1_kin'
, 'l_remle': 'l_remle_kin'
, 'ref_allele1': 'reference_allele'}, inplace = True)
# FIXME: should be at source
# checking tot_diff column
#print((dfm2_mis['tot_diff']==1).all()) and remove these cols
#3) drop some not required cols (including duplicate if you want)
#3a) drop duplicate columns
dfm2_mis2 = dfm2_mis.T.drop_duplicates().T #changes dtypes in cols, so not used
dup_cols = set(dfm2_mis.columns).difference(dfm2_mis2.columns)
print('Total no of duplciate columns:', len(dup_cols)
, '\nDuplicate columns identified:', dup_cols)
#dup_cols = {'alt_allele0', 'ps'} # didn't want to remove tot_diff
del(dfm2_mis2)
#print('removing duplicate columns: kept one of the dup_cols i.e tot_diff')
print('Removing duplicate columns'
, '\nOriginal dim:', dfm2_mis.shape)
dfm2_mis.drop(list(dup_cols), axis = 1, inplace = True)
print('\nRevised dim:', dfm2_mis.shape, 'after removing', len(dup_cols), 'columns')
#3b) other not useful columns
cols_to_drop = ['chromosome_text', 'n_diff', 'chr', 'symbol', '_merge' ]
dfm2_mis.drop(cols_to_drop, axis = 1, inplace = True)
#dfm2_mis.rename(columns = {'ref_allele1': 'reference_allele'}, inplace = True)
print('Dim after dropping', len(cols_to_drop), 'columns:', dfm2_mis.shape)
#print(dfm2_mis.columns)
#4) reorder columns
#orkin_linked = dfm2_mis.copy()
orkin_linked = dfm2_mis[['mutation',
'mutationinformation',
'wild_type',
'position',
'mutant_type',
'chr_num_allele',
'ref_allele',
'alt_allele',
'mut_info',
'mut_type',
'gene_id',
'gene_number',
'mut_region',
'reference_allele',
'alternate_allele',
'chromosome_number',
#'afs
'af_kin',
'or_kin',
# 'ors_logistic',
# 'ors_chi_cus',
# 'ors_fisher',
'pwald_kin',
# 'pvals_logistic',
# 'pvals_fisher',
# 'ci_lb_fisher',
# 'ci_ub_fisher' ,
'beta_kin',
'se_kin',
'logl_H1_kin',
'l_remle_kin',
# 'stat_chi',
# 'pvals_chi',
# 'n_diff',
# 'tot_diff',
'n_miss',
'wt_3let',
'mt_3let']]
# sanity check after reassigning columns
if orkin_linked.shape == dfm2_mis.shape and set(orkin_linked.columns) == set(dfm2_mis.columns):
print('PASS: Successfully formatted df with rearranged columns')
else:
sys.exit('FAIL: something went wrong when rearranging columns!')
#%% write file
print('\n====================================================================='
, '\nWriting output file:\n', outfile_or_kin
, '\nNo.of rows:', len(dfm2_mis)
, '\nNo. of cols:', len(dfm2_mis.columns))
orkin_linked.to_csv(outfile_or_kin, index = False)
#%% diff b/w allele0 and 1: or_df
#https://stackoverflow.com/questions/40348541/pandas-diff-with-string
#df = or_df.iloc[[5, 15, 17, 19, 34]]
#df[['alt_allele0','ref_allele1']].ne(df[['alt_allele0','ref_allele1']].shift()).any(axis=1).astype(int)
#df[['alt_allele0','ref_allele1']].ne(df[['alt_allele0','ref_allele1']].shift()).any(axis=1).astype(int)