From f4ebb07045dad2c6bce5a6ec42a54d6859bc1ddd Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Mon, 20 Sep 2021 16:12:45 +0100
Subject: [PATCH] split csv for isoniazid

---
 dynamut/split_csv.sh |   1 +
 mcsm/run_mcsm.py     |   2 +-
 my_header.R          | 107 ++++++++++++++++++++++++++++++++-----------
 3 files changed, 82 insertions(+), 28 deletions(-)

diff --git a/dynamut/split_csv.sh b/dynamut/split_csv.sh
index 17c1a03..1f7a793 100755
--- a/dynamut/split_csv.sh
+++ b/dynamut/split_csv.sh
@@ -19,5 +19,6 @@ split ../../${INFILE} -l ${CHUNK} -d snp_batch_
 #~/git/LSHTM_analysis/dynamut/split_csv.sh gid_mcsm_formatted_snps.csv snp_batches 50
 #~/git/LSHTM_analysis/dynamut/split_csv.sh embb_mcsm_formatted_snps.csv snp_batches 50
 #~/git/LSHTM_analysis/dynamut/split_csv.sh pnca_mcsm_formatted_snps.csv snp_batches 50
+#~/git/LSHTM_analysis/dynamut/split_csv.sh katg_mcsm_formatted_snps.csv snp_batches 50     #Date: 20/09/2021
 
 # add .txt to the files
diff --git a/mcsm/run_mcsm.py b/mcsm/run_mcsm.py
index 7e38543..da621f5 100755
--- a/mcsm/run_mcsm.py
+++ b/mcsm/run_mcsm.py
@@ -104,7 +104,7 @@ if mutation_filename:
     in_filename_snps = mutation_filename
 else:
     in_filename_snps = gene.lower() + '_mcsm_formatted_snps.csv'
-    
+   
 infile_snps = outdir + '/' + in_filename_snps
 
 #=======
diff --git a/my_header.R b/my_header.R
index 5009f29..2fa892c 100644
--- a/my_header.R
+++ b/my_header.R
@@ -1,21 +1,31 @@
 #########################################################
-### A) Installing and loading required packages
+# A) Installing and loading required packages
+# B) My functions
+#########################################################
+
 #########################################################
 #lib_loc = "/usr/local/lib/R/site-library")
 
-#if (!require("gplots")) {
-#  install.packages("gplots", dependencies = TRUE)
-#  library(gplots)
-#}
+require("getopt", quietly = TRUE) # cmd parse arguments
 
-#if (!require("tidyverse")) {
-#  install.packages("tidyverse", dependencies = TRUE)
-#  library(tidyverse)
-#}
+if (!require("tidyverse")) {
+  install.packages("tidyverse", dependencies = TRUE)
+  library(tidyverse)
+}
 
-if (!require("ggplot2")) {
-  install.packages("ggplot2", dependencies = TRUE)
-  library(ggplot2)
+if (!require("shiny")) {
+  install.packages("shiny", dependencies = TRUE)
+  library(shiny)
+}
+
+if (!require("shinyBS")) {
+  install.packages("shinyBS", dependencies = TRUE)
+  library(shinyBS)
+}
+
+if (!require("gridExtra")) {
+  install.packages("gridExtra", dependencies = TRUE)
+  library(gridExtra)
 }
 
 if (!require("ggridges")) {
@@ -23,6 +33,35 @@ if (!require("ggridges")) {
   library(ggridges)
 }
 
+# if (!require("ggplot2")) {
+#   install.packages("ggplot2", dependencies = TRUE)
+#   library(ggplot2)
+# }
+
+# if (!require ("dplyr")){
+#   install.packages("dplyr")
+#   library(dplyr)
+# }
+
+if (!require ("DT")){
+  install.packages("DT")
+  library(DT)
+}
+
+if (!require ("plyr")){
+   install.packages("plyr")
+   library(plyr)
+ }
+
+# Install
+#if(!require(devtools)) install.packages("devtools")
+#devtools::install_github("kassambara/ggcorrplot")
+
+if (!require ("ggbeeswarm")){
+   install.packages("ggbeeswarm")
+   library(ggbeeswarm)
+}
+
 if (!require("plotly")) {
   install.packages("plotly", dependencies = TRUE)
   library(plotly)
@@ -103,11 +142,6 @@ if (!require ("psych")){
   library(psych)
 }
 
-if (!require ("dplyr")){
-  install.packages("dplyr")
-  library(dplyr)
-}
-
 if (!require ("compare")){
   install.packages("compare")
   library(compare)
@@ -118,18 +152,37 @@ if (!require ("arsenal")){
   library(arsenal)
 }
 
+if(!require(ggseqlogo)){
+  install.packages("ggseqlogo")
+  library(ggseqlogo)
+}
 
-####TIDYVERSE
-# Install
-#if(!require(devtools)) install.packages("devtools")
-#devtools::install_github("kassambara/ggcorrplot")
-
-#library(ggcorrplot)
-
-
-###for PDB files
-#install.packages("bio3d") 
+# for PDB files
 if(!require(bio3d)){
   install.packages("bio3d")
   library(bio3d)
 }
+
+library(protr)
+if(!require(protr)){
+  install.packages("protr")
+  library(protr)
+}
+
+#if (!requireNamespace("BiocManager", quietly = TRUE))
+#  install.packages("BiocManager")
+
+#BiocManager::install("Logolas")
+library("Logolas")
+
+
+####################################
+# Load all my functions:
+# only works if tidyverse is loaded
+# hence included it here!
+####################################
+
+func_path = "~/git/LSHTM_analysis/scripts/functions/"
+source_files <- list.files(func_path, "\\.R$")  # locate all .R files
+map(paste0(func_path, source_files), source)  # source all your R scripts!
+