From 7982ce9cb56569aca2b59e5ac46fa45bd59098e1 Mon Sep 17 00:00:00 2001
From: teddyCodex <samted.uche@gmail.com>
Date: Tue, 8 Oct 2024 18:34:23 +0100
Subject: [PATCH] refactor function names in pre-msa-tree and reverse_operons

---
 R/pre-msa-tree.R    | 16 ++++++++--------
 R/reverse_operons.R | 12 ++++++------
 2 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/R/pre-msa-tree.R b/R/pre-msa-tree.R
index 44979c3c..833a1335 100644
--- a/R/pre-msa-tree.R
+++ b/R/pre-msa-tree.R
@@ -546,7 +546,7 @@ acc2fa <- function(accessions, outpath, plan = "sequential") {
     return(result)
 }
 
-#' RepresentativeAccNums
+#' createRepresentativeAccNum
 #'
 #' @description
 #' Function to generate a vector of one Accession number per distinct observation from 'reduced' column
@@ -566,7 +566,7 @@ acc2fa <- function(accessions, outpath, plan = "sequential") {
 #' @export
 #'
 #' @examples
-RepresentativeAccNums <- function(prot_data,
+createRepresentativeAccNum <- function(prot_data,
     reduced = "Lineage",
     accnum_col = "AccNum") {
     # Get Unique reduced column and then bind the AccNums back to get one AccNum per reduced column
@@ -623,15 +623,15 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
     )
 
     if (typeof(outpath) == "character") {
-        write.MsaAAMultipleAlignment(aligned, outpath)
+        writeMSAAAMultipleAlignment2FA(aligned, outpath)
     }
     return(aligned)
 }
 
-#' write.MsaAAMultipleAlignment
+#' writeMSAAAMultipleAlignment2FA
 #'
 #' @description
-#' Write MsaAAMultpleAlignment Objects as algined fasta sequence
+#' Write MsaAAMultpleAlignment Objects as aligned fasta sequence
 #' MsaAAMultipleAlignment Objects are generated from calls to msaClustalOmega
 #' and msaMuscle from the 'msa' package
 #'
@@ -647,7 +647,7 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
 #' @export
 #'
 #' @examples
-write.MsaAAMultipleAlignment <- function(alignment, outpath) {
+writeMSAAAMultipleAlignment2FA <- function(alignment, outpath) {
     l <- length(rownames(alignment))
     fasta <- ""
     for (i in 1:l)
@@ -660,7 +660,7 @@ write.MsaAAMultipleAlignment <- function(alignment, outpath) {
     return(fasta)
 }
 
-#' get_accnums_from_fasta_file
+#' getAccNumFromFA
 #'
 #' @param fasta_file
 #'
@@ -671,7 +671,7 @@ write.MsaAAMultipleAlignment <- function(alignment, outpath) {
 #' @export
 #'
 #' @examples
-get_accnums_from_fasta_file <- function(fasta_file) {
+getAccNumFromFA <- function(fasta_file) {
     txt <- read_file(fasta_file)
     accnums <- stringi::stri_extract_all_regex(fasta_file, "(?<=>)[\\w,.]+")[[1]]
     return(accnums)
diff --git a/R/reverse_operons.R b/R/reverse_operons.R
index e4bbd50e..a2570e8d 100755
--- a/R/reverse_operons.R
+++ b/R/reverse_operons.R
@@ -3,7 +3,7 @@
 # Modified by Janani Ravi and Samuel Chen
 
 
-#' reveql
+#' straightenOperonSeq
 #'
 #' @param prot
 #'
@@ -11,7 +11,7 @@
 #' @export
 #'
 #' @examples
-reveql <- function(prot) {
+straightenOperonSeq <- function(prot) {
     w <- prot # $GenContext.orig # was 'x'
 
     y <- rep(NA, length(w))
@@ -57,7 +57,7 @@ reveql <- function(prot) {
 
 ## The function to reverse operons
 
-#' reverse_operon
+#' reverseOperonSeq
 #'
 #' @param prot
 #'
@@ -65,7 +65,7 @@ reveql <- function(prot) {
 #' @export
 #'
 #' @examples
-reverse_operon <- function(prot) {
+reverseOperonSeq <- function(prot) {
     gencontext <- prot$GenContext
 
     gencontext <- gsub(pattern = ">", replacement = ">|", x = gencontext)
@@ -108,7 +108,7 @@ reverse_operon <- function(prot) {
 
 
 
-    ge <- lapply(1:length(ge), function(x) reveql(ge[[x]]))
+    ge <- lapply(1:length(ge), function(x) straightenOperonSeq(ge[[x]]))
 
     ye <- te[withouteq]
 
@@ -141,4 +141,4 @@ reverse_operon <- function(prot) {
 # colnames(prot) <- c("AccNum","GenContext.orig","len", "GeneName","TaxID","Species")
 
 ## ??? straighten operons
-# prot$GenContext.orig <- reverse_operon(prot)
+# prot$GenContext.orig <- reverseOperonSeq(prot)