R/alignmentFull.R

In HLAtools: Toolkit for HLA Immunogenomics

### Alignment Full v3.3.0 16 April 2024

################
##alignmentFull
#'Build Sets of Protein, Codon, Coding Nucleotide and Genomic Nucleotide Alignments for Specified  Loci
#'
#'Applies buildAlignments() to build a set of alignments for loci supported in the ANHIG/IMGTHLA GitHub repository.
#'
#'@param loci A characer vector of the locus names for which alignments should be built. The default value ("all") generates alignments for all loci. 
#'@param alignType A character vector of alignment types. The allowed values are "all", "prot", "codon", "nuc", and "gen", which specify either all available alignments for a given locus or the respective protein, codon, nucleotide and genomic alignments, as determined by the HLAgazeteer.
#'@param version A character string describing the version of the ANHIG/IMGTHLA Github repository from which alignments are obtained. The default value, 'HLAgazeteer$version', generates alignments for the IPD-IMGT/HLA Database release under which the HLAgazeteer was built.
#'
#'@return A list object containing data frames of protein (prot), codon (codon), coding nucleotide (nuc), or genomic nucleotide (gen) alignments, for specified genes in the specified IPD-IMGT/HLA Database release, along with the pertinent reference database release.
#'
#'@note AlignmentFull() must be run to build the 'HLAalignments' object (HLAalignments <- alignmentFull()) before other functions that use alignments can be used, and therefore requires internet access.
#'@note Depending on local download speeds, building all available alignments for all loci can take several minutes.
#'@note Prior to IPD-IMGT/HLA Database release version 3.24.0, the HLA-DP and HLA-DQ sequence alignment files in the IPD-IMGT/HLA GitHub Repository did not all include a numerical suffix in the gene name (e.g., the protein sequence alignment file for the DQA1 gene was named 'DQA_prot.txt') because alignment files for the DPA2, DPB2, DQA2 and DQB2 genes had not been made available. Building DPA1, DPB1, DQA1, and DQB1 sequence alignments from releases prior to 3.24.0 require using a gene name that does not include the numerical suffix.
#'
#'@export
#'
alignmentFull <- function(loci = "all", alignType = "all", version = HLAgazeteer$version) {
  
  if(!"all" %in% loci) {
      loci <- multiLocusValidation(loci) }
  
  if(!"all" %in% alignType) {
  alignType <- checkAlignType(alignType) }
  
  NL1 <- NL2 <- NL3 <- NL4 <- NULL
  
  if(version != "Latest"){ #
    if(!validateVersion(version)){stop(paste(version," is not a valid IPD-IMGT/HLA Database release version."))}
        } else{ version <- getLatestVersion()}

  if(length(loci) == 1 && loci == "all" && alignType == "all") {
  
  #list of loci names
  NL4 <- NL1 <- as.list(HLAgazeteer$nuc) #cDNA and codon
  NL2 <- as.list(HLAgazeteer$gen) #gDNA
  NL3 <- as.list(HLAgazeteer$prot) #AA
  
  } else {
  
    if("all" %in% alignType)  { 
      NL1 <- as.list(loci[loci %in% as.list(HLAgazeteer$nuc)]) #nuc 
      NL2 <- as.list(loci[loci %in% as.list(HLAgazeteer$gen)]) #gen
      NL3 <- as.list(loci[loci %in% as.list(HLAgazeteer$prot)]) #prot
      NL4 <- as.list(loci[loci %in% as.list(HLAgazeteer$nuc)]) # codon
        } else {
            if("nuc" %in% alignType)  { NL1 <- as.list(loci[loci %in% as.list(HLAgazeteer$nuc)]) } #nuc 
            if("gen" %in% alignType)  { NL2 <- as.list(loci[loci %in% as.list(HLAgazeteer$gen)]) } #gen 
            if("prot" %in% alignType)  { NL3 <- as.list(loci[loci %in% as.list(HLAgazeteer$prot)]) } # prot
            if("codon" %in% alignType)  { NL4 <- as.list(loci[loci %in% as.list(HLAgazeteer$nuc)]) } # codon
          }
    
      }

  #creating nested lists for cDNA, gDNA and amino acid
  cList <- vector(mode='list', length=length(NL1))
  gList <- vector(mode='list', length=length(NL2))
  protList <- vector(mode='list', length=length(NL3))
  codonList <- vector(mode='list', length=length(NL4))

  #filling nested lists with alignments
#  if(NL1 != "") {
    if(length(NL1) > 0) { 
      for(i in 1:length(NL1)){
        cList[i] <- suppressWarnings(buildAlignments(as.character(NL1[i]), "cDNA", version = version)[[1]][2]) } 
    
        names(cList) <- NL1
      }
#    }
#  if(NL2 != "") {
    if(length(NL2) > 0) { 
      for(i in 1:length(NL2)){
        gList[i] <- suppressWarnings(buildAlignments(as.character(NL2[i]), "gDNA", version = version)[[1]][1]) }
    
        names(gList) <- NL2
      }
#    }
#  if(NL3 != "") {
    if(length(NL3) > 0) { 
      for(i in 1:length(NL3)){
        protList[i] <- suppressWarnings(buildAlignments(as.character(NL3[i]), "AA", version = version)[[1]][1]) }
    
        names(protList) <- NL3
      }
#    }
#  if(NL4 != "") {
    if(length(NL4) > 0) { 
      for(i in 1:length(NL4)){
        codonList[i] <- suppressWarnings(buildAlignments(as.character(NL4[i]), "cDNA", version = version)[[1]][1]) }
    
        names(codonList) <- NL4
      }
#    }

  #placing nested lists inside of larger list
  AllAlignment<-list(firstList <- protList,
                 fourthlist <- codonList,
                 secondList <- cList,
                 thirdlist <- gList,
                 versionString <- version)
#naming nested lists

  names(AllAlignment) <- c("prot","codon","nuc","gen","version")

  AllAlignment
}