moved all test scripts for functions to tests/

scripts/functions/test_af_or_calcs.R

@@ -1,59 +0,0 @@
-#!/usr/bin/env Rscript                                                  
-#########################################################
-# TASK: To calculate Allele Frequency and
-# Odds Ratio from master data
-#########################################################
-# load libraries
-#source("Header_TT.R")
-require("getopt", quietly = TRUE) # cmd parse arguments
-
-# working dir and loading libraries
-getwd()
-setwd("~/git/LSHTM_analysis/scripts/functions/")
-getwd()
-
-# load functions
-source("plotting_globals.R")
-source("mychisq_or.R")
-source("myaf_or_calcs.R")
-
-# cmd options + sensible defaults
-drug = "streptomycin"
-gene = "gid"
-
-# call function
-import_dirs(drug, gene)
-
-# input file 1: master data
-#in_filename_master  = 'original_tanushree_data_v2.csv' #19K
-in_filename_master  = 'mtb_gwas_meta_v6.csv' #35k
-infile_master = paste0(datadir, in_filename_master)
-cat(paste0('Reading infile1: raw data', ' ', infile_master) )
-
-# input file 2: gene associated meta data file to extract valid snps and add calcs to.
-# This is outfile_metadata from data_extraction.py
-in_filename_metadata =  paste0(tolower(gene), '_metadata.csv')
-infile_metadata = paste0(outdir, '/', in_filename_metadata)
-cat(paste0('Reading input file 2 i.e gene associated metadata:', infile_metadata))
-
-# out_filename_af_or = paste0(tolower(gene), '_meta_data_with_AF_OR.csv')
-out_filename_af_or = paste0(tolower(gene), '_af_or.csv')
-outfile_af_or = paste0(outdir, '/', out_filename_af_or)
-cat(paste0('Output file with full path:', outfile_af_or))
-
-cat("master data:", infile_master)
-cat("gene data:", infile_metadata)
-
-dr_muts_col # comes from global (dr_mutations_<drug>)
-other_muts_col # comes from global (other_mutations_<drug>)
-#################################################
-my_afor (  infile_master
-         , infile_metadata
-         , outfile = outfile_af_or
-         #, outfile = "FOO_TEST.csv"
-         , drug
-         , gene
-         , idcol = "id"
-         , dr_muts_col 
-         , other_muts_col
-         )