Merge pull request JRaviLab#87 from teddyCodex/issue-52-rename-functions

refactor function names in R/pre-msa-tree and R/reverse-operons.R
- fixes JRaviLab#52

NAMESPACE

@@ -4,16 +4,13 @@ export(BinaryDomainNetwork)
 export(GCA2Lineage)
 export(GenContextNetwork)
 export(IPG2Lineage)
-export(RepresentativeAccNums)
 export(acc2FA)
 export(acc2Lineage)
 export(acc2fa)
 export(addLeaves2Alignment)
 export(addLineage)
 export(addName)
 export(addTaxID)
-export(add_leaves)
-export(add_name)
 export(advanced_opts2est_walltime)
 export(alignFasta)
 export(assign_job_queue)
@@ -31,11 +28,11 @@ export(convert2TitleCase)
 export(convertAlignment2FA)
 export(convertAlignment2Trees)
 export(convertFA2Tree)
-export(convert_aln2fa)
 export(countByColumn)
 export(createFA2Tree)
 export(createJobResultsURL)
 export(createJobStatusEmailMessage)
+export(createRepresentativeAccNum)
 export(createWordCloud2Element)
 export(createWordCloudElement)
 export(create_lineage_lookup)
@@ -49,15 +46,13 @@ export(findParalogs)
 export(formatJobArgumentsHTML)
 export(gc_undirected_network)
 export(generateAllAlignments2FA)
-export(generate_all_aln2fa)
 export(generate_msa)
+export(getAccNumFromFA)
 export(getTopAccByLinDomArch)
-export(get_accnums_from_fasta_file)
 export(get_proc_medians)
 export(get_proc_weights)
 export(make_opts2procs)
 export(mapAcc2Name)
-export(map_acc2name)
 export(map_advanced_opts2procs)
 export(msa_pdf)
 export(plotIPR2Viz)
@@ -83,26 +78,25 @@ export(removeTails)
 export(renameFA)
 export(rename_fasta)
 export(replaceQuestionMarks)
-export(reveql)
-export(reverse_operon)
+export(reverseOperonSeq)
 export(run_deltablast)
 export(run_rpsblast)
 export(selectLongestDuplicate)
 export(sendJobStatusEmail)
 export(shortenLineage)
 export(sinkReset)
+export(straightenOperonSeq)
 export(summarizeByLineage)
 export(summarizeDomArch)
 export(summarizeDomArch_ByLineage)
 export(summarizeGenContext)
 export(summarizeGenContext_ByDomArchLineage)
 export(summarizeGenContext_ByLineage)
 export(themeGenes2)
-export(to_titlecase)
 export(totalGenContextOrDomArchCounts)
 export(validateCountDF)
 export(wordcloud3)
-export(write.MsaAAMultipleAlignment)
+export(writeMSA_AA2FA)
 export(write_proc_medians_table)
 export(write_proc_medians_yml)
 importFrom(Biostrings,AAStringSet)

R/CHANGED-pre-msa-tree.R

@@ -54,7 +54,7 @@ convert2TitleCase <- function(x, y = " ") {
 ################################
 ## Function to add leaves to an alignment file
 ## !! Add DA to leaves?
-#' Adding Leaves to an alignment file w/ accessions
+#' addLeaves2Alignment
 #'
 #' @author Janani Ravi
 #' @keywords alignment, accnum, leaves, lineage, species
@@ -178,7 +178,7 @@ addLeaves2Alignment <- function(aln_file = "",
 }
 
 
-#' Add Name
+#' addName
 #'
 #' @author Samuel Chen, Janani Ravi
 #' @description This function adds a new 'Name' column that is comprised of components from
@@ -252,7 +252,7 @@ addName <- function(data,
 
 ################################
 ## Function to convert alignment 'aln' to fasta format for MSA + Tree
-#' Adding Leaves to an alignment file w/ accessions
+#' convertAlignment2FA
 #'
 #' @author Janani Ravi
 #' @keywords alignment, accnum, leaves, lineage, species
@@ -320,6 +320,9 @@ convertAlignment2FA <- function(aln_file = "",
     return(fasta)
 }
 
+#' mapAcc2Name
+#' 
+#' @description
 #' Default renameFA() replacement function. Maps an accession number to its name
 #'
 #' @param line The line of a fasta file starting with '>'
@@ -382,6 +385,9 @@ renameFA <- function(fa_path, outpath,
 
 ################################
 ## generateAllAlignments2FA
+#' generateAllAlignments2FA
+#' 
+#' @description 
 #' Adding Leaves to an alignment file w/ accessions
 #'
 #' @keywords alignment, accnum, leaves, lineage, species
@@ -441,10 +447,11 @@ generateAllAlignments2FA <- function(aln_path = here("data/rawdata_aln/"),
 
 # accessions <- c("P12345","Q9UHC1","O15530","Q14624","P0DTD1")
 # accessions <- rep("ANY95992.1", 201)
-#' acc2FA converts protein accession numbers to a fasta format.
+#' acc2FA 
 #'
 #' @description
-#' Resulting fasta file is written to the outpath.
+#' converts protein accession numbers to a fasta format. Resulting 
+#' fasta file is written to the outpath.
 #'
 #' @author Samuel Chen, Janani Ravi
 #' @keywords accnum, fasta
@@ -539,6 +546,9 @@ acc2FA <- function(accessions, outpath, plan = "sequential") {
     return(result)
 }
 
+#' createRepresentativeAccNum
+#' 
+#' @description
 #' Function to generate a vector of one Accession number per distinct observation from 'reduced' column
 #'
 #' @author Samuel Chen, Janani Ravi
@@ -556,7 +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
@@ -585,6 +595,9 @@ RepresentativeAccNums <- function(prot_data,
     return(accessions)
 }
 
+#' alignFasta
+#' 
+#' @description
 #' Perform a Multiple Sequence Alignment on a FASTA file.
 #'
 #' @author Samuel Chen, Janani Ravi
@@ -610,12 +623,12 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
     )
 
     if (typeof(outpath) == "character") {
-        write.MsaAAMultipleAlignment(aligned, outpath)
+        writeMSA_AA2FA(aligned, outpath)
     }
     return(aligned)
 }
 
-#' Write MsaAAMultpleAlignment Objects as algined fasta sequence
+#' writeMSA_AA2FA
 #'
 #' @description
 #' MsaAAMultipleAlignment Objects are generated from calls to msaClustalOmega
@@ -632,7 +645,7 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
 #' @export
 #'
 #' @examples
-write.MsaAAMultipleAlignment <- function(alignment, outpath) {
+writeMSA_AA2FA <- function(alignment, outpath) {
     l <- length(rownames(alignment))
     fasta <- ""
     for (i in 1:l)
@@ -645,7 +658,7 @@ write.MsaAAMultipleAlignment <- function(alignment, outpath) {
     return(fasta)
 }
 
-#' Get accnums from fasta file
+#' getAccNumFromFA
 #'
 #' @param fasta_file
 #'
@@ -655,7 +668,7 @@ 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)

R/pre-msa-tree.R

@@ -49,7 +49,7 @@ api_key <- Sys.getenv("ENTREZ_API_KEY", unset = "YOUR_KEY_HERE")
 #' @export
 #'
 #' @examples
-to_titlecase <- function(x, y = " ") {
+convert2TitleCase <- function(x, y = " ") {
     s <- strsplit(x, y)[[1]]
     paste(toupper(substring(s, 1, 1)), substring(s, 2),
         sep = "", collapse = y
@@ -59,7 +59,7 @@ to_titlecase <- function(x, y = " ") {
 ################################
 ## Function to add leaves to an alignment file
 ## !! Add DA to leaves?
-#' Adding Leaves to an alignment file w/ accessions
+#' addLeaves2Alignment
 #'
 #' @author Janani Ravi
 #'
@@ -95,9 +95,9 @@ to_titlecase <- function(x, y = " ") {
 #'
 #' @examples
 #' \dontrun{
-#' add_leaves("pspa_snf7.aln", "pspa.txt")
+#' addLeaves2Alignment("pspa_snf7.aln", "pspa.txt")
 #' }
-add_leaves <- function(aln_file = "",
+addLeaves2Alignment <- function(aln_file = "",
     lin_file = "data/rawdata_tsv/all_semiclean.txt", # !! finally change to all_clean.txt!!
     # lin_file="data/rawdata_tsv/PspA.txt",
     reduced = FALSE) {
@@ -184,7 +184,7 @@ add_leaves <- function(aln_file = "",
 }
 
 
-#' Title
+#' addName
 #'
 #' @author Samuel Chen, Janani Ravi
 #'
@@ -209,7 +209,7 @@ add_leaves <- function(aln_file = "",
 #' @export
 #'
 #' @examples
-add_name <- function(data,
+addName <- function(data,
     accnum_col = "AccNum", spec_col = "Species", lin_col = "Lineage",
     lin_sep = ">", out_col = "Name") {
     cols <- c(accnum_col, "Kingdom", "Phylum", "Genus", "Spp")
@@ -258,7 +258,7 @@ add_name <- function(data,
 
 ################################
 ## Function to convert alignment 'aln' to fasta format for MSA + Tree
-#' Adding Leaves to an alignment file w/ accessions
+#' convertAlignment2FA
 #'
 #' @author Janani Ravi
 #'
@@ -288,9 +288,9 @@ add_name <- function(data,
 #'
 #' @examples
 #' \dontrun{
-#' add_leaves("pspa_snf7.aln", "pspa.txt")
+#' convertAlignment2FA("pspa_snf7.aln", "pspa.txt")
 #' }
-convert_aln2fa <- function(aln_file = "",
+convertAlignment2FA <- function(aln_file = "",
     lin_file = "data/rawdata_tsv/all_semiclean.txt", # !! finally change to all_clean.txt!!
     fa_outpath = "",
     reduced = FALSE) {
@@ -324,6 +324,9 @@ convert_aln2fa <- function(aln_file = "",
     return(fasta)
 }
 
+#' mapAcc2Name
+#' 
+#' @description
 #' Default rename_fasta() replacement function. Maps an accession number to its name
 #'
 #' @param line he line of a fasta file starting with '>'
@@ -340,7 +343,7 @@ convert_aln2fa <- function(aln_file = "",
 #' @export
 #'
 #' @examples
-map_acc2name <- function(line, acc2name, acc_col = "AccNum", name_col = "Name") {
+mapAcc2Name <- function(line, acc2name, acc_col = "AccNum", name_col = "Name") {
     # change to be the name equivalent to an add_names column
     # Find the first ' '
     end_acc <- str_locate(line, " ")[[1]]
@@ -386,7 +389,10 @@ rename_fasta <- function(fa_path, outpath,
 }
 
 ################################
-## generate_all_aln2fa
+## generateAllAlignments2FA
+#' generateAllAlignments2FA
+#' 
+#' @description
 #' Adding Leaves to an alignment file w/ accessions
 #'
 #' @author Janani Ravi
@@ -413,9 +419,9 @@ rename_fasta <- function(fa_path, outpath,
 #'
 #' @examples
 #' \dontrun{
-#' generate_all_aln2fa()
+#' generateAllAlignments2FA()
 #' }
-generate_all_aln2fa <- function(aln_path = here("data/rawdata_aln/"),
+generateAllAlignments2FA <- function(aln_path = here("data/rawdata_aln/"),
     fa_outpath = here("data/alns/"),
     lin_file = here("data/rawdata_tsv/all_semiclean.txt"),
     reduced = F) {
@@ -448,6 +454,10 @@ generate_all_aln2fa <- function(aln_path = here("data/rawdata_aln/"),
 # accessions <- rep("ANY95992.1", 201)
 #' acc2fa
 #'
+#' @description
+#' converts protein accession numbers to a fasta format. Resulting 
+#' fasta file is written to the outpath.
+#' 
 #' @author Samuel Chen, Janani Ravi
 #' @keywords accnum, fasta
 #'
@@ -546,7 +556,7 @@ 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 +576,7 @@ 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 +633,15 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
     )
 
     if (typeof(outpath) == "character") {
-        write.MsaAAMultipleAlignment(aligned, outpath)
+        writeMSA_AA2FA(aligned, outpath)
     }
     return(aligned)
 }
 
-#' write.MsaAAMultipleAlignment
+#' writeMSA_AA2FA
 #'
 #' @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 +657,7 @@ alignFasta <- function(fasta_file, tool = "Muscle", outpath = NULL) {
 #' @export
 #'
 #' @examples
-write.MsaAAMultipleAlignment <- function(alignment, outpath) {
+writeMSA_AA2FA <- function(alignment, outpath) {
     l <- length(rownames(alignment))
     fasta <- ""
     for (i in 1:l)
@@ -660,7 +670,7 @@ write.MsaAAMultipleAlignment <- function(alignment, outpath) {
     return(fasta)
 }
 
-#' get_accnums_from_fasta_file
+#' getAccNumFromFA
 #'
 #' @param fasta_file
 #'
@@ -671,7 +681,7 @@ 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)