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# parse dnv table to HGNC, columns:
# Reauired: VarID, Score, HGNC, aaChg
# Optional: offset
source('./parse.input.table/parse.variant.wt.sequence.R')
dnv.table.to.uniprot.by.af2.uniprotID.parallel <- function(
dnv.table, VarID.column, Score.column,
uniprotID.column, aaChg.column, offset.column=NA, length.column=NA,
match.length=FALSE, njobs=96) {
library(doParallel)
cl <- makeCluster(njobs)
registerDoParallel(cl)
if (!is.na(offset.column)) {
offset <- as.numeric(dnv.table[,offset.column])
} else {
offset <- rep(0, dim(dnv.table)[1])
}
offset[is.na(offset)] <- 0
if (match.length) {
prompt <- data.frame(VarID = dnv.table[,VarID.column],
aaChg = dnv.table[,aaChg.column],
score = dnv.table[,Score.column],
uniprotID = dnv.table[,uniprotID.column],
seq.match.length = dnv.table[,length.column])
} else {
prompt <- data.frame(VarID = dnv.table[,VarID.column],
aaChg = dnv.table[,aaChg.column],
score = dnv.table[,Score.column],
uniprotID = dnv.table[,uniprotID.column])
}
uniprot_ID.mapping <- read.csv('./parse.input.table/swissprot_and_human.full.seq.csv')
# order to make sure first use longest transcript
# uniprot_ID.mapping <- uniprot_ID.mapping[order(uniprot_ID.mapping$Length, decreasing = T),]
result <- foreach (i = 1:dim(prompt)[1], .combine = rbind, .multicombine=TRUE) %dopar% {
source('./parse.input.table/parse.variant.wt.sequence.R')
substitute_res <- list(ref=NA, pos=NA, alt=NA, wt = NA,
sequence = NA, sequence.len = NA,
seq.start = NA, seq.end = NA,
pos.orig = NA, sequence.orig = NA,
wt.orig = NA, sequence.len.orig = NA)
aaChg <- prompt$aaChg[i]
uniprot_IDs <- prompt$uniprotID[i]
if (grepl("-", uniprot_IDs) | !uniprot_IDs %in% uniprot_ID.mapping$uniprotID) {
url.request <- paste0('https://rest.uniprot.org/uniprotkb/', uniprot_IDs, '.fasta')
txt <- strsplit(RCurl::getURL(url.request), split = '\n')[[1]]
wt.sequences <- paste(txt[2:length(txt)], collapse = '')
} else {
wt.sequences <- uniprot_ID.mapping$seq[match(uniprot_IDs, uniprot_ID.mapping$uniprotID)]
}
if (match.length) {
if (!is.na(wt.sequences) & nchar(wt.sequences) != prompt$seq.match.length[i]) {
wt.sequences <- NA
}
}
j = 1
while (is.na(substitute_res$sequence) & j <= length(uniprot_IDs)) {
matched_uniprot_ID <- uniprot_IDs[j]
wt.sequence <- wt.sequences[j]
# parse variant
substitute_res <- parse_one_substitute(aaChg, wt.sequence, offset[i])
j = j + 1
}
tmp <- data.frame(VarID = prompt$VarID[i],
aaChg = prompt$aaChg[i],
uniprotID = matched_uniprot_ID,
ref = substitute_res$ref,
pos = substitute_res$pos,
alt = substitute_res$alt,
score = prompt$score[i],
sequence = substitute_res$sequence,
wt = substitute_res$wt,
sequence.len = substitute_res$sequence.len,
seq.start = substitute_res$seq.start,
seq.end = substitute_res$seq.end,
pos.orig = substitute_res$pos.orig,
sequence.orig = substitute_res$sequence.orig,
wt.orig = substitute_res$wt.orig,
sequence.len.orig = substitute_res$sequence.len.orig)
tmp
}
stopCluster(cl)
dnv.table$place.holder <- NA
result <- dplyr::bind_cols(result, dnv.table[,!colnames(dnv.table) %in% colnames(result)])
result$place.holder <- NULL
result.noNA <- result[!is.na(result$sequence),]
output <- list(result=result,
result.noNA=result.noNA)
output
}
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