From 7686aa39b489846557e3779342c6f099f6acd37c Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Fri, 11 Jun 2021 13:33:25 +0100
Subject: [PATCH] added script to test af_or_calcs

---
 .../{af_or_calcs.R => myaf_or_calcs.R}        |  0
 scripts/functions/test_af_or_calcs.R          | 55 +++++++++++++++++++
 .../functions/{test_functions.R => test_bp.R} |  0
 3 files changed, 55 insertions(+)
 rename scripts/functions/{af_or_calcs.R => myaf_or_calcs.R} (100%)
 create mode 100644 scripts/functions/test_af_or_calcs.R
 rename scripts/functions/{test_functions.R => test_bp.R} (100%)

diff --git a/scripts/functions/af_or_calcs.R b/scripts/functions/myaf_or_calcs.R
similarity index 100%
rename from scripts/functions/af_or_calcs.R
rename to scripts/functions/myaf_or_calcs.R
diff --git a/scripts/functions/test_af_or_calcs.R b/scripts/functions/test_af_or_calcs.R
new file mode 100644
index 0000000..d48bfef
--- /dev/null
+++ b/scripts/functions/test_af_or_calcs.R
@@ -0,0 +1,55 @@
+#!/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
+
+
+# load functions
+source("functions/plotting_globals.R")
+source("functions/mychisq_or.R")
+source("functions/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
+         )
diff --git a/scripts/functions/test_functions.R b/scripts/functions/test_bp.R
similarity index 100%
rename from scripts/functions/test_functions.R
rename to scripts/functions/test_bp.R