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128 lines
4.3 KiB
R
128 lines
4.3 KiB
R
# Installing dependencies
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dependencies <- c("stringi", "doParallel")
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missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
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if(length(missing_packages)) install.packages(missing_packages)
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rm(missing_packages,dependencies)
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IsolateCanonicalVariant <- function (AAchangeAnnotations){
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# #<---------------------------->
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# # You must include this section when:
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# # Distributing, Using and/or Modifying this code.
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# # Please read and abide by the terms of the included LICENSE.
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# # Copyright 2020, Deepankar Chakroborty, All rights reserved.
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# #
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# # Author : Deepankar Chakroborty (https://github.com/dchakro)
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# # Website: https://www.dchakro.com
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# # Report issues: https://github.com/dchakro/shared_Rscripts/issues
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# # License: https://github.com/dchakro/shared_Rscripts/blob/master/LICENSE
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# #<---------------------------->
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# # PURPOSE:
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# # From a given vector of annotations for a particular DNA change
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# # this function selects the canonical variant (if present)
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# # by cross referencing the MANE Select and RefSeq Select sets.
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# # LOGIC FLOW:
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# # - If there is only one annotation; that is selected
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# # - If canonical transcript is not found in MANE Select + RefSeq select
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# # or a matching transcript ID is not found in the annotation then;
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# # The mutation with to the the highest position (residue number) is selected.
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# # - If a match for canonical isoform is found then;
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# # that particular mutation is selected
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# importing resources
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library(doParallel)
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refseq <- readRDS(url("https://raw.githubusercontent.com/dchakro/shared_Rscripts/master/asset/RefSeqSelect_Gene_Transcript.RDS"),"rb")
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source("https://raw.githubusercontent.com/dchakro/shared_Rscripts/master/MutSiteFind.R")
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# initializing cluster
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myCluster <- makeCluster(parallel::detectCores(),
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type = "FORK",
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useXDR=F,
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.combine=cbind)
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registerDoParallel(myCluster)
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print(myCluster)
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file.create("log.txt")
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message(paste0("Logging processed mutations at: ",getwd(),"/log.txt"))
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# computation
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results <- foreach(MutInfo = AAchangeAnnotations,.combine = c) %dopar% {
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GENE <- can.isoform <- l <- l2 <- NA
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l=unique(unlist(
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stringi::stri_split_fixed(
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str = MutInfo,
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pattern = ","),
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use.names = F,
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recursive = F))
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if(length(l)==1){
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l2 <- unlist(stringi::stri_split_fixed(
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str = l,
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pattern = ":"),
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use.names = F,
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recursive = F)
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MUTATION <- stringi::stri_replace_first_fixed(
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str = l2[stringi::stri_detect_regex(
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str = l2,
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use.names = F,
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pattern = "^p\\.")],
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pattern = "p.",
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replacement = "")
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} else {
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GENE <- stringi::stri_sub(
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str = l[1],
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from = 1,
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to = stringi::stri_locate_first_fixed(
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str = l[1],
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pattern = ":")[,"end"]-1)
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can.isoform <- refseq$transcript_accession[refseq$gene_id==GENE]
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if(length(can.isoform)==0 | !any(stringi::stri_detect_fixed(str = l,pattern = can.isoform))){
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# Canonical isoform not found in RefSeq, or Match for Canonical isoform not found in AAchangeAnnotations
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l2 <- unlist(
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stringi::stri_split_fixed(
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str = l,
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pattern = ":"),
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use.names = F,
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recursive = F)
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l3 <- stringi::stri_replace_all_fixed(
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str = l2[stringi::stri_startswith_fixed(
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str = l2,
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"p.")],
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pattern = "p.",
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replacement = "")
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MUTATION <- l3[which.max(MutSiteFind(l3))]
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} else {
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# Canonical isoform found
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l=l[grep(can.isoform,l)]
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l2 <- unlist(
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stringi::stri_split_fixed(
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str = l,
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pattern = ":"),
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use.names = F,
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recursive = F)
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MUTATION <- stringi::stri_replace_first_fixed(
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str = l2[stringi::stri_detect_regex(
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str = l2,
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use.names = F,
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pattern = "^p\\.")],
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pattern = "p.",
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replacement = "")
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}
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}
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if(length(MUTATION)==0){
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MUTATION <- NA
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}
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cat(paste(MUTATION,"\n"),file="log.txt", append=T)
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return(MUTATION)
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}
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stopCluster(myCluster)
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return(results)
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}
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