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Merge branch 'develop'

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This commit is contained in:
Deepankar Chakroborty 2020-07-30 10:53:35 +03:00
commit 36b51322d5
1 changed files with 61 additions and 9 deletions
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70
IsolateCanonicalVariant.R
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@ -34,7 +34,12 @@ IsolateCanonicalVariant <- function (AAchangeAnnotations){
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)
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"))
@ -42,24 +47,71 @@ IsolateCanonicalVariant <- function (AAchangeAnnotations){
# 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))
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 = "")
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)
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 = "")
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 = "")
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){