From 584ae98360c3dd9010bc23d96fc7251f3b13cbfd Mon Sep 17 00:00:00 2001
From: dchakro <35454738+dchakro@users.noreply.github.com>
Date: Wed, 31 May 2023 09:51:31 -0700
Subject: [PATCH] updates

---
 .Rhistory      | 73 ++++++++++++++++++++++++++++++++++++++++++++++++++
 r.snippets.txt |  9 +++++++
 2 files changed, 82 insertions(+)
 create mode 100644 .Rhistory

diff --git a/.Rhistory b/.Rhistory
new file mode 100644
index 0000000..479669f
--- /dev/null
+++ b/.Rhistory
@@ -0,0 +1,73 @@
+unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
+# Installing missing dependencies
+dependencies <- c("stringi", "progress")
+missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
+if(length(missing_packages)) install.packages(missing_packages)
+# Sanity checks
+check_paralog_sep <- !any(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
+check_annotation_sep <- !any(stringi::stri_detect_fixed(str =  DATA$AAChange.refGene, pattern = annotation_separator))
+idx_Gene <- which(colnames(DATA) == GeneColName)
+idx_Annotation <- which(colnames(DATA) == AnnotationColName)
+if(length(idx_Gene) == 0 | length(idx_Annotation) == 0 | check_paralog_sep | check_annotation_sep) {
+message(stringi::stri_c("You entered :-->",
+"\nparalog_separator = ",paralog_separator,
+"\nannotation_separator = ",annotation_separator,
+"\nGeneColName = ", GeneColName,
+"\nAnnotationColName = ",AnnotationColName))
+stop("Inconsistencies with these input parameters.\n Ensure they are correct and try again.")
+}
+# Cleanup
+rm(missing_packages,dependencies,check_paralog_sep,check_annotation_sep)
+gc()
+current.idx <- nrow(DATA)+1
+paralog.idx <- which(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
+pb <- progress::progress_bar$new(total=length(paralog.idx),format = " [:bar] :current/:total (:percent)",); pb$tick(0)
+Number_of_paralogs <- sum(stringi::stri_count_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
+message(stringi::stri_c("There are ",length(paralog.idx)," annotations with ", Number_of_paralogs," paralogs."))
+# copying structure of original DATA
+DATA.add <- DATA[1,]; DATA.add <- DATA.add[-1,]
+# Adding the empty rows to original table.
+# These rows will be populated in the for loop
+DATA.add <- dplyr::bind_rows(DATA.add,data.frame(matrix(nrow = (length(paralog.idx)+Number_of_paralogs), ncol = ncol(DATA),dimnames = list(c(),colnames(DATA))),stringsAsFactors = F))
+DATA <- dplyr::bind_rows(DATA,DATA.add)
+rm(DATA.add) ; gc()
+# Beginning isolation of the paralogs
+for(i in paralog.idx){
+Muts <- unlist(stringi::stri_split_fixed(DATA$AAChange.refGene[i],annotation_separator),use.names = F,recursive = F)
+for (gene in unlist(stringi::stri_split_fixed(DATA$Gene.refGene[i],pattern = paralog_separator),use.names = F,recursive = F)){
+DATA[current.idx,] <- DATA[i,]
+DATA$Gene.refGene[current.idx] <- gene
+DATA$AAChange.refGene[current.idx] <- paste0(Muts[grep(gene,Muts,fixed = T)],collapse=",")
+current.idx <- current.idx+1
+}
+pb$tick(1)
+}
+# removing the original rows with the paralogs as they are all unparalogged now
+DATA <- DATA[-paralog.idx,]
+rownames(DATA) <- as.character(seq(1,length(DATA[,1])))
+return (DATA)
+}
+dependencies <- c("stringi")
+missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
+if(length(missing_packages)) install.packages(missing_packages)
+rm(missing_packages,dependencies)
+MutSiteFind <- function(MutationColumn){
+# #<---------------------------->
+# # Please include this section when distributing and/or using this code.
+# # Please read and abide by the terms of the included LICENSE.
+# # Copyright 2020, Deepankar Chakroborty
+# #
+# #  Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
+# #  Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
+# #  License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
+# #
+# #  PURPOSE:
+# #  For a given vector of amino acid changes like A123T, V256F, E746_A750del
+# #  this function returns c(123, 256, 746) as amino acid positions of
+# #  the mutated residue.
+# #     In case of indels, it doesn't return the range!! (returns only the start position)
+# #
+# #<---------------------------->
+return(unlist(x = stringi::stri_extract_first_regex(str = MutationColumn,pattern = "[[:digit:]]+"), use.names = F))
+}
+MutSiteFind
diff --git a/r.snippets.txt b/r.snippets.txt
index 7626464..a92ef8c 100644
--- a/r.snippets.txt
+++ b/r.snippets.txt
@@ -9,6 +9,15 @@ snippet beginr
 	rm(list = ls())
 	gc()
 	library(data.table)
+	today <- format(Sys.Date(),format = "%Y-%m-%d")
+	slug <- "${2:SubFolderName}"
+	workingDirectory <- paste0(today,"_",slug)
+	setwd("~/ANALYSIS/")
+	ifelse(test = dir.exists(workingDirectory), 
+		yes = message(paste0(workingDirectory," exists...")),
+		no = dir.create(workingDirectory))
+	setwd(workingDirectory)
+	rm(today,workingDirectory,slug)
 	${0}
 
 snippet comment_date