tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

renamed files & added or kinship link file

Browse source
This commit is contained in:
Tanushree Tunstall 2020-06-19 10:33:26 +01:00
parent c36197d75e
commit 07258120de
3 changed files with 646 additions and 0 deletions
Download patch file Download diff file Expand all files Collapse all files

0
scripts/AF_and_OR_calcs.R → scripts/af_or_calcs.R
View file

385
scripts/af_or_calcs_scratch.R Normal file
View file

@ -0,0 +1,385 @@
#########################################################
# TASK: To compare OR from master data
# chisq, fisher test and logistic and adjusted logistic
#########################################################
getwd()
setwd('~/git/LSHTM_analysis/scripts')
getwd()
#install.packages("logistf")
library(logistf)
#########################################################
#%% variable assignment: input and output paths & filenames
drug = 'pyrazinamide'
gene = 'pncA'
gene_match = paste0(gene,'_p.')
cat(gene_match)
#===========
# input and output dirs
#===========
datadir = paste0('~/git/Data')
indir = paste0(datadir, '/', drug, '/', 'input')
outdir = paste0(datadir, '/', drug, '/', 'output')
#===========
# input and output files
#===========
in_filename = 'original_tanushree_data_v2.csv'
#in_filename = 'mtb_gwas_v3.csv'
infile = paste0(datadir, '/', in_filename)
cat(paste0('Reading infile1: raw data', ' ', infile) )
# infile2: _gene associated meta data file to extract valid snps and add calcs to.
# This is outfile3 from data_extraction.py
in_filename_metadata = paste0(tolower(gene), '_metadata.csv')
infile_metadata = paste0(outdir, '/', in_filename_metadata)
cat(paste0('Reading infile2: gene associated metadata:', infile_metadata))
#===========
# output
#===========
out_filename = paste0(tolower(gene),'_', 'meta_data_with_AF_OR.csv')
outfile = paste0(outdir, '/', out_filename)
cat(paste0('Output file with full path:', outfile))
#%% end of variable assignment for input and output files
#########################################################
# 1: Read master/raw data stored in Data/
#####################################################
#===============
# Step 1: read raw data (all remove entries with NA in pza column)
#===============
raw_data_all = read.csv(infile, stringsAsFactors = F)
# building cols to extract
dr_muts_col = paste0('dr_mutations_', drug)
other_muts_col = paste0('other_mutations_', drug)
cat('Extracting columns based on variables:\n'
, drug
, '\n'
, dr_muts_col
, '\n'
, other_muts_col
, '\n===============================================================')
raw_data = raw_data_all[,c("id"
, drug
, dr_muts_col
, other_muts_col)]
rm(raw_data_all)
rm(indir, in_filename, infile)
#===========
# 1a: exclude na
#===========
raw_data = raw_data[!is.na(raw_data[[drug]]),]
total_samples = length(unique(raw_data$id))
cat(paste0('Total samples without NA in', ' ', drug, 'is:', total_samples))
# sanity check: should be true
is.numeric(total_samples)
#===========
# 1b: combine the two mutation columns
#===========
#raw_data$all_mutations_pyrazinamide = paste(raw_data$dr_mutations_pyrazinamide, raw_data$other_mutations_pyrazinamide)
all_muts_colname = paste0('all_mutations_', drug)
raw_data[[all_muts_colname]] = paste(raw_data[[dr_muts_col]], raw_data[[other_muts_col]])
head(raw_data[[all_muts_colname]])
#===========
# 1c: create yet another column that contains all the mutations but in lower case
#===========
head(raw_data[[all_muts_colname]])
raw_data$all_muts_gene = tolower(raw_data[[all_muts_colname]])
head(raw_data$all_muts_gene)
# sanity checks
#table(grepl("gene_p",raw_data$all_muts_gene))
cat(paste0('converting gene match:', gene_match, ' ', 'to lowercase'))
gene_match = tolower(gene_match)
table(grepl(gene_match,raw_data$all_muts_gene))
# sanity check
if(sum(table(grepl(gene_match, raw_data$all_muts_gene))) == total_samples){
cat('PASS: Total no. of samples match')
} else{
cat('FAIL: No. of samples mismatch')
}
#########################################################
# 2: Read valid snps for which OR
# can be calculated
#########################################################
cat(paste0('Reading metadata infile:', infile_metadata))
gene_metadata = read.csv(infile_metadata
#, file.choose()
, stringsAsFactors = F
, header = T)
# clear variables
rm(in_filename_metadata, infile_metadata)
# count na in pyrazinamide column
tot_pza_na = sum(is.na(gene_metadata$pyrazinamide))
expected_rows = nrow(gene_metadata) - tot_pza_na
# drop na from the pyrazinamide colum
gene_snps_or = gene_metadata[!is.na(gene_metadata[[drug]]),]
# sanity check
if(nrow(gene_snps_or) == expected_rows){
cat('PASS: no. of rows match with expected_rows')
} else{
cat('FAIL: nrows mismatch.')
}
# extract unique snps to iterate over for AF and OR calcs
gene_snps_unique = unique(gene_snps_or$mutation)
cat(paste0('Total no. of distinct comp snps to perform OR calcs: ', length(gene_snps_unique)))
#=====================================
#OR calcs using the following 4
#1) chisq.test
#2) fisher
#3) modified chisq.test
#4) logistic
#5) adjusted logistic?
#6) kinship (separate script)
#======================================
################# modified chisq OR
# Define OR function
#x = as.numeric(mut)
#y = dst
my_chisq_or = function(x,y){
tab = as.matrix(table(x,y))
a = tab[2,2]
if (a==0){ a<-0.5}
b = tab[2,1]
if (b==0){ b<-0.5}
c = tab[1,2]
if (c==0){ c<-0.5}
d = tab[1,1]
if (d==0){ d<-0.5}
(a/b)/(c/d)
}
#========================
# TEST WITH ONE
i = "pnca_p.trp68gly"
i = "pnca_p.gln10pro"
i = "pnca_p.leu159arg"
# IV
table(grepl(i,raw_data$all_muts_gene))
mut = grepl(i,raw_data$all_muts_gene)
# DV
#dst = raw_data$pyrazinamide
dst = raw_data[[drug]] # or raw_data[,drug]
# 2X2 table
table(mut, dst)
# CV
#c = raw_data$id[mut]
c = raw_data$id[grepl(i,raw_data$all_muts_gene)]
#sid = grepl(raw_data$id[mut], raw_data$id) # warning
#argument 'pattern' has length > 1 and only the first element will be used
#grepl(raw_data$id=="ERR2512440", raw_data$id)
sid = grepl(paste(c,collapse="|"), raw_data$id)
table(sid)
# 3X2 table
table(mut, dst, sid)
#============================
# compare OR
chisq.test(table(mut,dst))
fisher.test(table(mut, dst))
fisher.test(table(mut, dst))$p.value
fisher.test(table(mut, dst))$estimate
my_chisq_or(mut,dst)
# logistic or
summary(model<-glm(dst ~ mut, family = binomial))
or_logistic = exp(summary(model)$coefficients[2,1]); print(or_logistic)
pval_logistic = summary(model)$coefficients[2,4]; print(pval_logistic)
# adjusted logistic or
summary(model2<-glm(dst ~ mut + sid, family = binomial))
or_logistic2 = exp(summary(model2)$coefficients[2,1]); print(or_logistic2)
pval_logistic2 = summary(model2)$coefficients[2,4]; print(pval_logistic2)
#=========================
ors = sapply(gene_snps_unique,function(m){
mut = grepl(m,raw_data$all_muts_gene)
my_chisq_or(mut,dst)
})
ors
pvals = sapply(gene_snps_unique,function(m){
mut = grepl(m,raw_data$all_muts_gene)
fisher.test(mut,dst)$p.value
})
pvals
afs = sapply(gene_snps_unique,function(m){
mut = grepl(m,raw_data$all_muts_gene)
mean(mut)
})
afs
# logistic
logistic_ors = sapply(gene_snps_unique,function(m){
mut = grepl(m,raw_data$all_muts_gene)
model<-glm(dst ~ mut, family = binomial)
or_logistic = exp(summary(model)$coefficients[2,1])
#pval_logistic = summary(model)$coefficients[2,4]
})
logistic_ors
# logistic adj # Doesn't seem to make a difference
logistic_ors2 = sapply(gene_snps_unique,function(m){
mut = grepl(m,raw_data$all_muts_gene)
c = raw_data$id[mut]
sid = grepl(paste(c,collapse="|"), raw_data$id)
model2<-glm(dst ~ mut + sid, family = binomial)
or_logistic2 = exp(summary(model2)$coefficients[2,1])
#pval_logistic2 = summary(model2)$coefficients[2,4]
})
logistic_ors2
or_logistic2; pval_logistic2
head(logistic_ors)
#====================================
# logistic
summary(model<-glm(dst ~ mut
, family = binomial
#, control = glm.control(maxit = 1)
#, options(warn = 1)
))
or_logistic_maxit = exp(summary(model)$coefficients[2,1]); print(or_logistic_maxit)
pval_logistic_maxit = summary(model)$coefficients[2,4]; print(pval_logistic_maxit)
#####################
# iterate: subset
#####################
snps_test = c("pnca_p.trp68gly", "pnca_p.leu4ser", "pnca_p.leu159arg","pnca_p.his57arg" )
data = snps_test[1:2]
data
################# start loop
for (i in data){
print(i)
# IV
#mut<-as.numeric(grepl(i,raw_data$all_muts_gene))
mut = grepl(i,raw_data$all_muts_gene)
table(mut)
# DV
#dst<-as.numeric(raw_data[[drug]])
dst = raw_data[[drug]]
# table
print(table(dst, mut))
#=====================
# logistic regression, glm.control(maxit = n)
#https://stats.stackexchange.com/questions/11109/how-to-deal-with-perfect-separation-in-logistic-regression
#=====================
#n = 1
summary(model<-glm(dst ~ mut
, family = binomial
#, control = glm.control(maxit = 1)
#, options(warn = 1)
))
or_logistic_maxit = exp(summary(model)$coefficients[2,1]); print(or_logistic_maxit)
pval_logistic_maxit = summary(model)$coefficients[2,4]; print(pval_logistic_maxit)
#=====================
# fishers test
#=====================
#attributes(fisher.test(table(dst, mut)))
or_fisher = fisher.test(table(dst, mut))$estimate
or_fisher = or_fisher[[1]]; or_fisher
pval_fisher = fisher.test(table(dst, mut))$p.value ; pval_fisher
#=====================
# chi square
#=====================
#chisq.test(y = dst, x = mut)
#attributes(chisq.test(table(dst, mut)))
est_chisq = chisq.test(table(dst, mut))$statistic
est_chisq = est_chisq[[1]]; est_chisq
pval_chisq = chisq.test(table(dst, mut))$p.value; pval_chisq
# all output
writeLines(c(paste0("mutation:", i)
, paste0("=========================")
, paste0("OR_logistic_maxit:", or_logistic_maxit,"--->", "P-val_logistic_maxit:", pval_logistic_maxit )
, paste0("OR_fisher:", or_fisher, "--->","P-val_fisher:", pval_fisher )
, paste0("Chi_sq_estimate:", est_chisq, "--->","P-val_chisq:", pval_chisq)))
}
i = "gene_p.leu159arg"
mut<-as.numeric(grepl(i,raw_data$all_muts_pza))
# DV
dst<-as.numeric(raw_data$pyrazinamide)
# tablehttps://mail.google.com/mail/?tab=rm&ogbl
table(dst, mut)
#=====================
# fishers test
#=====================
#attributes(fisher.test(table(dst, mut)))
or_fisher = fisher.test(table(dst, mut))$estimate
or_fisher = or_fisher[[1]]; or_fisher
pval_fisher = fisher.test(table(dst, mut))$p.value ; pval_fisher
# https://stats.stackexchange.com/questions/259635/what-is-the-difference-using-a-fishers-exact-test-vs-a-logistic-regression-for
exact2x2(table(dst, mut),tsmethod="central")

261
scripts/or_kinship_link.py Executable file
View file

@ -0,0 +1,261 @@
#!/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
#%%
import os, sys
import pandas as pd
#import numpy as np
import re
from find_missense import find_missense
import argparse
#%%
# homedir
homedir = os.path.expanduser('~')
#os.chdir(homedir + '/git/Misc/jody_pza')
#=======================================================================
#%% command line args
arg_parser = argparse.ArgumentParser()
#arg_parser.add_argument('-d', '--drug', help='drug name', default = 'pyrazinamide')
#arg_parser.add_argument('-g', '--gene', help='gene name', default = 'pncA') # case sensitive
arg_parser.add_argument('-d', '--drug', help = 'drug name', default = None)
arg_parser.add_argument('-g', '--gene', help = 'gene name (case sensitive)', default = None) # case sensitive
#arg_parser.add_argument('-p', '--outpath', help = 'output path', default = outpath)
#arg_parser.add_argument('-o', '--outfile', help = 'output filename', default = outfile_or_kin)
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
args = arg_parser.parse_args()
#=======================================================================
#%% variables
#or_file
#info_file
#short_info_file
#gene = 'pncA'
#drug = 'pyrazinamide'
start_cds = args.start_coord
end_cds = args.end_coord
gene = args.gene
drug = args.drug
#=======================================================================
#%% input and output dirs and files
#=======
# data dir
#=======
datadir = homedir + '/' + 'git/Data'
indir = datadir + '/' + drug + '/input'
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'
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'
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 = '\t', 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 = ['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
#start_cds = 2288681
#end_cds = 2289241
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:
print('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
#FIXME: Turn to a function
orig_len = len(or_df.columns)
#find_missense(or_df, 'ref_allele1', 'alt_allele0')
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))
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:
print('FAIL: some genomic locs or_df chr number DO NOT have meta data in snp_info.txt')
#%% Perform merge
#join_type = 'inner'
#join_type = 'outer'
join_type = 'left'
#join_type = 'right'
#dfm1 = pd.merge(or_df, info_df, on ='chromosome_number', how = join_type, indicator = True) # not unique!
dfm1 = pd.merge(or_df, info_df, on = ['chromosome_number', 'ref_allele', 'alt_allele'], how = join_type, 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 = join_type, indicator = True)
dfm2['_merge'].value_counts()
# count no. of nan
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
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:
print('FAIL: Second cross check unsuccessfull. Debug please!')
sys.exit()
orig_len = len(dfm2_mis.columns)
#%% extract mut info into three cols
dfm2_mis['wild_type'] = dfm2_mis['mut_info'].str.extract('(\w{1})>')
dfm2_mis['position'] = dfm2_mis['mut_info'].str.extract('(\d+)')
dfm2_mis['mutant_type'] = dfm2_mis['mut_info'].str.extract('>\d+(\w{1})')
dfm2_mis['mutationinformation'] = dfm2_mis['wild_type'] + dfm2_mis['position'] + dfm2_mis['mutant_type']
# sanity check
ncols_add = 4
if len(dfm2_mis.columns) == orig_len + ncols_add:
print('PASS: Succesfully extracted and added mutationinformation(mcsm style)')
else:
print('FAIL: No. of cols mismatch'
,'\noriginal length:', orig_len
, '\nExpected no. of cols:', orig_len + ncols_add
, '\nGot no. of cols:', len(dfm2_mis.columns))
sys.exit()
#%% write file
print('Writing output file:\n', outfile_or_kin
, '\nNo.of rows:', len(dfm2_mis)
, '\nNo. of cols:', len(dfm2_mis.columns))
dfm2_mis.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)