140 lines
4.6 KiB
R
Executable file
140 lines
4.6 KiB
R
Executable file
#!/usr/bin/env Rscript
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#########################################################
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# TASK: To calculate Allele Frequency and
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# Odds Ratio from master data
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#########################################################
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# working dir
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setwd("~/git/LSHTM_analysis/scripts")
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getwd()
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# load libraries
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#source("~/git/LSHTM_analysis/scripts/Header_TT.R")
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require("getopt", quietly = TRUE) # cmd parse arguments
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# load functions
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source("functions/plotting_globals.R")
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source("functions/mychisq_or.R")
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source("functions/myaf_or_calcs.R")
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#############################################################
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# command line args
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#********************
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spec = matrix(c(
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"drug" ,"d", 1, "character",
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"gene" ,"g", 1, "character",
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"master_data" ,"m", 2, "character",
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"gene_data" ,"G", 2, "character",
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"outfile" ,"o", 2, "character",
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"idcol" ,"I", 2, "character",
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"drmuts_col" ,"D", 2, "character",
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"othermuts_col" ,"O", 2, "character"
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), byrow = TRUE, ncol = 4)
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opt = getopt(spec)
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drug = opt$drug
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gene = opt$gene
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infile_master = opt$master_data
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infile_metadata = opt$gene_data
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outfile = opt$outfile
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idcol = opt$idcol
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dr_muts_col = opt$drmuts_col
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other_muts_col = opt$othermuts_col
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if(is.null(drug)|is.null(gene)) {
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stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
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}
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# import_dirs()
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import_dirs(drug, gene)
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# setting sensible defaults for opt args
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#----------------------------
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# input file 1: master data
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#----------------------------
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#class(infile_master)
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if (is.null(infile_master)){
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#if (!is.character(infile) && exists("gene")){
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#in_filename_master = 'original_tanushree_data_v2.csv' #19K
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in_filename_master = 'mtb_gwas_meta_v6.csv' #35k
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infile_master = paste0(datadir, in_filename_master)
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cat("\nInput file 1 not specified, assuming filename: ", infile_master)
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cat(paste0("\nReading infile 1 i.e raw data: ", infile_master) )
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}
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#---------------------------------------------------
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# input file 2: gene associated meta
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# data file to extract valid snps and add calcs to.
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#---------------------------------------------------
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if (is.null(infile_metadata)){
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# This is outfile_metadata from data_extraction.py
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in_filename_metadata = paste0(tolower(gene), '_metadata.csv')
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infile_metadata = paste0(outdir, '/', in_filename_metadata)
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cat("\nInput file 2 not specified, assuming filename: ", infile_metadata)
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cat(paste0("\nReading infile 2 i.e gene associated metadata:", infile_metadata))
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}
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#-------------------------------------------
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# outfile: csv file containing AF and OR
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#-------------------------------------------
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if (is.null(outfile)){
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# out_filename_af_or = paste0(tolower(gene), '_meta_data_with_AF_OR.csv')
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out_filename_af_or = paste0(tolower(gene), '_af_or.csv')
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outfile = paste0(outdir, '/', out_filename_af_or)
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cat("\nOutfile not specified, assuming filename: ", outfile)
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cat(paste0('\nOutput file with full path:', outfile))
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}
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#-------------------------------------------
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# idcol: column name "id"
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#-------------------------------------------
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if (is.null(idcol)){
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idcol = "id"
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}
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#-------------------------------------------
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# dr-and-others muts cols: comes from plotting_globals.R
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# colnames that can be constructed using drug
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# (dr_mutations_<drug>), (other_mutations_<drug>)
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#-------------------------------------------
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if (is.null(dr_muts_col)){
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dr_muts_col
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cat("\ndrug and other mut colnames not specified, sourcing from globals: "
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, dr_muts_col, "\n")
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}
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if (is.null(other_muts_col)){
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other_muts_col
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cat("\ndrug and other mut colnames not specified, sourcing from globals: "
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, other_muts_col, "\n")
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}
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# Informing the user of the sensible defaults being used:
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cat("======================"
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, "\nParameters passed:"
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, "\n======================"
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, "\nDRUG name: ", drug, "\n"
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, "\nGENE name: ", gene, "\n"
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, "\nReading infile 1 i.e raw data: ", infile_master, "\n"
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, "\nReading infile 2 i.e gene associated metadata:", infile_metadata, "\n"
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, '\nOutput file with full path:', outfile, "\n"
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, "\nColumn name of id:", idcol, "\n"
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, "\ndr mutation colname:", dr_muts_col, "\n"
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, "\nother mutation colname:", other_muts_col, "\n")
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#=======================================================================
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#============================
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# call function: my_afor()
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#=============================
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my_afor( drug
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, gene
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, infile_master
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, infile_metadata
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, outfile
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, idcol
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, dr_muts_col
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, other_muts_col
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)
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#=======================================================================
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