Updates

- add IsolateCanonicalVariant.R
- remove variables used to check and install dependencies

IsolateCanonicalVariant.R

@@ -0,0 +1,74 @@
+# #<---------------------------->
+# # Please include this section when distributing and/or using this code. 
+# # Please read and abide by the terms of the included LICENSE
+# #
+# #  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:
+# #  From a given vector of annotations for a particular DNA change
+# #  this function selects the canonical variant (if present)
+# #  by cross referencing the MANE Select and RefSeq Select sets.
+# #
+# #  Logic flow:
+# #  - If there is only one annotation; that is selected
+# #  - If canonical transcript is not found in MANE Select + RefSeq select 
+# #     or a matching transcript ID is not found in the annotation then;
+# #     The mutation with to the the highest position (residue number) is selected.
+# #  - If a match for canonical isoform is found then; 
+# #        that particular mutation is selected
+# #
+# #<---------------------------->
+
+# Installing dependencies
+dependencies <- c("stringi", "doParallel")
+missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
+if(length(missing_packages)) install.packages(missing_packages) 
+rm(missing_packages,dependencies)
+
+IsolateCanonicalVariant <- function (AAchangeAnnotations){
+  library(doParallel)
+  #--- Change to master when ready
+  # importing resources
+  refseq <- readRDS(url("https://gitlab.utu.fi/deecha/shared_scripts/-/raw/develop/asset/RefSeqSelect_Gene_Transcript.RDS"),"rb")
+  source("https://gitlab.utu.fi/deecha/shared_scripts/-/raw/master/MutSiteFind.R")
+  
+  # initializing cluster
+  myCluster <- makeCluster(parallel::detectCores(), type = "FORK",useXDR=F,.combine=cbind); registerDoParallel(myCluster);print(myCluster)
+  
+  file.create("log.txt")
+  message(paste0("Logging processed mutations at: ",getwd(),"/log.txt"))
+  
+  # computation
+  results <- foreach(MutInfo = AAchangeAnnotations,.combine = c) %dopar% {
+    GENE <- can.isoform <- l <- l2 <- NA
+    l=unique(unlist(stringi::stri_split_fixed( str = MutInfo, pattern = ","),use.names = F,recursive = F))
+    
+    if(length(l)==1){
+      l2 <- unlist(stringi::stri_split_fixed( str = l, pattern = ":"),use.names = F,recursive = F)
+      MUTATION <- stringi::stri_replace_first_fixed(str = l2[stringi::stri_detect_regex(str = l2, use.names = F, pattern = "^p\\.")],pattern = "p.",replacement = "")
+    } else {
+      GENE <- stringi::stri_sub(str = l[1],from = 1,to = stringi::stri_locate_first_fixed(str = l[1],pattern = ":")[,"end"]-1)
+      can.isoform <- refseq$transcript_accession[refseq$gene_id==GENE]
+      if(length(can.isoform)==0 | !any(stringi::stri_detect_fixed(str = l,pattern = can.isoform))){
+        # Canonical isoform not found in RefSeq, or Match for Canonical isoform not found in AAchangeAnnotations
+        l2 <- unlist(stringi::stri_split_fixed( str = l, pattern = ":"),use.names = F,recursive = F)
+        l3 <- stringi::stri_replace_all_fixed(str = l2[stringi::stri_startswith_fixed(str = l2,"p.")],pattern = "p.",replacement = "")
+        MUTATION <- l3[which.max(MutSiteFind(l3))]
+      } else {
+        # Canonical isoform found
+        l=l[grep(can.isoform,l)]
+        l2 <- unlist(stringi::stri_split_fixed( str = l, pattern = ":"),use.names = F,recursive = F)
+        MUTATION <- stringi::stri_replace_first_fixed(str = l2[stringi::stri_detect_regex(str = l2, use.names = F, pattern = "^p\\.")],pattern = "p.",replacement = "")
+      }
+    }
+    if(length(MUTATION)==0){
+      MUTATION <- NA
+    }
+    cat(paste(MUTATION,"\n"),file="log.txt", append=T)
+    return(MUTATION)
+  }
+  stopCluster(myCluster)
+  return(results)
+}

MutSiteFind.R

@@ -17,6 +17,7 @@
 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){
   return(unlist(x = stringi::stri_extract_first_regex(str = MutationColumn,pattern = "[[:digit:]]+"), use.names = F))

unparalogMutations.R

@@ -33,6 +33,7 @@
 dependencies <- c("stringi", "progress")
 missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
 if(length(missing_packages)) install.packages(missing_packages)
+rm(missing_packages,dependencies)
 
 unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
    # Sanity checks
@@ -51,7 +52,7 @@ unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",",
    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)
+   rm(check_paralog_sep,check_annotation_sep)
    gc()
    
    current.idx <- 1 # nrow(DATA)+1