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server.R
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server.R
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library(stringr); library(plyr);
mypasswd = "asdfghjkl;'"
system('git config --global user.name "venyao"')
system('git config --global user.email "ywhzau@gmail.com"')
all.gene.info <- read.table("all.gene.info", head=T, as.is=T)
fetchPubmedById <- function(id="") {
url <- "https://pubmed.ncbi.nlm.nih.gov/"
finalUrl <- paste(url, id, '/?format=pubmed', sep='')
urlRes <- readLines(finalUrl)
if (any(grepl("^LID", urlRes, ignore.case=FALSE))) {
journal <- urlRes[grepl("^TA\\s", urlRes, ignore.case = FALSE)]
journal <- gsub(".+-\\s", "", journal)
title.start <- which(grepl("^TI\\s", urlRes, ignore.case = FALSE))
title.end <- which(grepl("^PG\\s", urlRes, ignore.case = FALSE))
if (length(title.end) == 0) {
title.end <- which(grepl("^LID\\s", urlRes, ignore.case = FALSE))[1]
}
title <- urlRes[title.start:(title.end - 1)]
title <- gsub(".+-\\s", "", title)
title <- gsub("^\\s+", "", title)
title <- paste(title, collapse = "", sep="")
year <- urlRes[grepl("^DEP\\s", urlRes, ignore.case = FALSE)]
if (length(year) == 0) {
year <- urlRes[grepl("^PHST", urlRes, ignore.case = FALSE)][1]
}
year <- gsub(".+-\\s", "", year)
year <- substr(year, 1, 4)
abstract.start <- which(grepl("^AB\\s", urlRes, ignore.case = FALSE))
abstract.end <- which(grepl("^CI\\s", urlRes, ignore.case = FALSE))
if (length(abstract.end) == 0) {
abstract.end <- which(grepl("^FAU\\s", urlRes, ignore.case = FALSE))[1]
}
abstract <- urlRes[abstract.start:(abstract.end - 1)]
abstract <- gsub(".+-\\s", "", abstract)
abstract <- gsub("^\\s+", "", abstract)
abstract <- paste(abstract, collapse = "", sep="")
affiliation.start <- which(grepl("^AD\\s", urlRes, ignore.case = FALSE))[1]
affiliation.end <- affiliation.start
for (i in (affiliation.start+1):(affiliation.start+10)) {
if (grepl("^\\s+", urlRes[i])) {
affiliation.end <- i
} else {
break
}
}
affiliation <- urlRes[affiliation.start:affiliation.end]
affiliation <- gsub(".+-\\s", "", affiliation)
affiliation <- gsub("^\\s+", "", affiliation)
affiliation <- paste(affiliation, collapse = "", sep="")
return(c(journal, title, year, affiliation, abstract))
} else {
return(c("", "", "", "", ""))
}
}
load("RiceNet_V2_GS.RData")
names(ricenet) <- c("Gene1", "Gene2")
load("rapmsu.rda")
ref.info <- read.table("reference.table", head=T, as.is=T, sep="\t",
quote="", comment="")
fam.gene.info <- read.table("famInfo.table", head=T, sep="\t", as.is=T)
fam.gene.msu <- 1:nrow(fam.gene.info)
names(fam.gene.msu) <- fam.gene.info$MSU
fam.gene.msu <- fam.gene.msu[names(fam.gene.msu)!="None"]
fam.gene.msu.new <- sapply(names(fam.gene.msu), function(x) {
x.name <- unlist(strsplit(x, split='|', fixed=TRUE))
if (length(x.name)==1) {
return(fam.gene.msu[x])
} else {
y <- rep(fam.gene.msu[x], length(x.name))
names(y) <- x.name
return(y)
}
})
fam.gene.msu.final <- unlist(unname(fam.gene.msu.new))
fam.gene.rap <- 1:nrow(fam.gene.info)
names(fam.gene.rap) <- fam.gene.info$RAPdb
fam.gene.rap <- fam.gene.rap[names(fam.gene.rap)!="None"]
fam.gene.rap.new <- sapply(names(fam.gene.rap), function(x) {
x.name <- unlist(strsplit(x, split='|', fixed=TRUE))
if (length(x.name)==1) {
return(fam.gene.rap[x])
} else {
y <- rep(fam.gene.rap[x], length(x.name))
names(y) <- x.name
return(y)
}
})
fam.gene.rap.final <- unlist(unname(fam.gene.rap.new))
gene.info <- read.table("geneInfo.table", head=T, sep="\t", as.is=T, quote="")
gene.keyword <- read.table("geneKeyword.table", head=T,
sep="\t", as.is=T, quote="", comment="")
RAPdb <- unique(gene.keyword[, c(2, 4)])
names(RAPdb)[1] <- "gene"
MSU <- unique(gene.keyword[, c(3:4)])
names(MSU)[1] <- "gene"
all.keyword <- rbind(RAPdb, MSU)
all.keyword <- all.keyword[all.keyword$gene!="None", ]
all.key <- unique(gene.keyword$Keyword)
all.sym <- sapply(gene.info$Symbol, function(x) {
symb <- unlist(strsplit(x, split="|", fixed=TRUE))
return(symb)
})
all.sym <- unlist(all.sym)
names(all.sym) <- NULL
gene.msu <- 1:nrow(gene.info)
names(gene.msu) <- gene.info$MSU
gene.msu <- gene.msu[names(gene.msu)!="None"]
gene.msu.new <- sapply(names(gene.msu), function(x) {
x.name <- unlist(strsplit(x, split='|', fixed=TRUE))
if (length(x.name)==1) {
return(gene.msu[x])
} else {
y <- rep(gene.msu[x], length(x.name))
names(y) <- x.name
return(y)
}
})
gene.msu.final <- unlist(unname(gene.msu.new))
gene.rap <- 1:nrow(gene.info)
names(gene.rap) <- gene.info$RAPdb
gene.rap <- gene.rap[names(gene.rap)!="None"]
gene.rap.new <- sapply(names(gene.rap), function(x) {
x.name <- unlist(strsplit(x, split='|', fixed=TRUE))
if (length(x.name)==1) {
return(gene.rap[x])
} else {
y <- rep(gene.rap[x], length(x.name))
names(y) <- x.name
return(y)
}
})
gene.rap.final <- unlist(unname(gene.rap.new))
#### publication
fetchRefByKey <- function(keyword="") {
keyword <- gsub("^\\s+", "", keyword)
keyword <- gsub(" +$", "", keyword)
keyword <- tolower(keyword)
if (nchar(keyword)<1) {
return(NULL)
} else {
datRes <- ref.info[grepl(keyword, ref.info$Title)|grepl(keyword, ref.info$Abstract, ignore.case=TRUE), ]
if (nrow(datRes)>0) {
return(datRes)
} else {
return(NULL)
}
}
}
#### MSU
fetchInfoByMsu <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.msu.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
gene.fl <- paste(path, "gene.info", sep="/")
if (file.exists(gene.fl)) {
dat <- read.table(gene.fl, head=T, sep="\t", as.is=T)
msu <- unlist(strsplit(dat$MSU, split='|', fixed=TRUE))
msu.new <- sapply(msu, function(x){
if (x!="None") {
y <- paste("http://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
msu.new <- paste(unname(msu.new), sep="", collapse="|")
dat$MSU <- msu.new
rap <- unlist(strsplit(dat$RAPdb, split='|', fixed=TRUE))
rap.new <- sapply(rap, function(x){
if (x!="None") {
y <- paste("https://rapdb.dna.affrc.go.jp/locus/?name=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
rap.new <- paste(unname(rap.new), sep="", collapse="|")
dat$RAPdb <- rap.new
return(dat)
}
} else {
return(NULL)
}
}
fetchFamInfoByMsu <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- fam.gene.msu.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
dat <- fam.gene.info[locus.line, ]
msu <- unlist(strsplit(dat$MSU, split='|', fixed=TRUE))
msu.new <- sapply(msu, function(x){
if (x!="None") {
y <- paste("http://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
msu.new <- paste(unname(msu.new), sep="", collapse="|")
dat$MSU <- msu.new
rap <- unlist(strsplit(dat$RAPdb, split='|', fixed=TRUE))
rap.new <- sapply(rap, function(x){
if (x!="None") {
y <- paste("https://rapdb.dna.affrc.go.jp/locus/?name=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
rap.new <- paste(unname(rap.new), sep="", collapse="|")
dat$RAPdb <- rap.new
dat$path <- NULL
return(dat)
} else {
return(NULL)
}
}
fetchRefByMsu <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.msu.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
ref.fl <- paste(path, "reference.info", sep="/")
if (file.exists(ref.fl)) {
dat <- read.table(ref.fl, head=T, sep="\t", as.is=T,
quote="", comment="")
dat$Publication <- NULL
dat$Affiliation <- NULL
for (i in 1:nrow(dat)) {
title <- dat$Title[i]
dat$Title[i] <- paste("https://www.ncbi.nlm.nih.gov/pubmed",
'?term=(', dat$Title[i],'%5BTitle%5D',
')', sep='')
dat$Title[i] <- paste('<a href="', dat$Title[i], '" target="_blank">', title,
'</a>', sep="")
dat$Title[i] <- HTML(dat$Title[i])
}
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
fetchFamRefByMsu <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- fam.gene.msu.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- fam.gene.info$path[locus.line]
ref.fl <- paste(path, "family.ref", sep="/")
if (file.exists(ref.fl)) {
dat <- read.table(ref.fl, head=T, sep="\t", as.is=T,
quote="", comment="")
dat$Affiliation <- NULL
for (i in 1:nrow(dat)) {
title <- dat$Title[i]
dat$Title[i] <- paste("https://www.ncbi.nlm.nih.gov/pubmed",
'?term=(', dat$Title[i],'%5BTitle%5D',
')', sep='')
dat$Title[i] <- paste('<a href="', dat$Title[i], '" target="_blank">', title,
'</a>', sep="")
dat$Title[i] <- HTML(dat$Title[i])
}
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
fetchAccByMsu <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.msu.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
acc.fls <- list.files(path, patter="*acc-*", full=T)
if (length(acc.fls)>0) {
acc.fls <- gsub(".+-", "", acc.fls)
acc.fls <- sapply(acc.fls, function(x){
y <- paste("https://www.ncbi.nlm.nih.gov/nuccore/", x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
})
dat <- data.frame(Accession=acc.fls, stringsAsFactors=FALSE)
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
fetchExpByMsu <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.msu.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
exp.fl <- paste(path, "expression.info", sep="/")
if (file.exists(exp.fl)) {
dat <- read.table(exp.fl, head=T, sep="\t", as.is=T)
return(dat)
}
} else {
return(NULL)
}
}
fetchTextByMsu <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.msu.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
text.fls <- list.files(path, patter="^pub.text.mining$", full=T)
if (length(text.fls)>0) {
text.con <- readLines(text.fls)
text.con <- text.con[!grepl("^symbol:", text.con)]
clone <- sapply(seq(2, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^cloning:\\s+", "", y)
return(y)
})
tdna <- sapply(seq(4, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^tdna:\\s+", "", y)
return(y)
})
tos <- sapply(seq(5, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^tos:\\s+", "", y)
return(y)
})
homo <- sapply(seq(6, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^homol:\\s+", "", y)
return(y)
})
rnai <- sapply(seq(7, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^rnai:\\s+", "", y)
return(y)
})
ove <- sapply(seq(8, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^ove:\\s+", "", y)
return(y)
})
rt <- sapply(seq(9, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^rt:\\s+", "", y)
return(y)
})
north <- sapply(seq(10, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^N:\\s+", "", y)
return(y)
})
south <- sapply(seq(11, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^S:\\s+", "", y)
return(y)
})
west <- sapply(seq(12, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^W:\\s+", "", y)
return(y)
})
access <- sapply(seq(3, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^access:\\s+", "", y)
return(y)
})
locus <- sapply(seq(1, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^locus:\\s+", "", y)
return(y)
})
dat <- data.frame(Cloning=clone, TDNA=tdna, Tos17=tos, Homolog=homo,
RNAi=rnai, Overexp=ove, RTPCR=rt, Northern=north,
Southern=south, Western=west, Locus=locus,
Accession=access,
stringsAsFactors=FALSE)
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
fetchKeyByMsu <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.msu.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
key.fl <- paste(path, "Keyword.trait", sep="/")
if (file.exists(key.fl)) {
dat <- read.table(key.fl, head=T, sep="\t", as.is=T,
quote="", comment="")
for (i in 1:nrow(dat)) {
title <- dat$Title[i]
dat$Title[i] <- paste("https://www.ncbi.nlm.nih.gov/pubmed",
'?term=(', dat$Title[i],'%5BTitle%5D',
')', sep='')
dat$Title[i] <- paste('<a href="', dat$Title[i], '" target="_blank">', title,
'</a>', sep="")
dat$Title[i] <- HTML(dat$Title[i])
}
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
fetchConneByMsu <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.msu.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
conne.fl <- paste(path, "Connection", sep="/")
if (file.exists(conne.fl)) {
dat <- read.table(conne.fl, head=F, sep="\t", as.is=T,
quote="", comment="")
names(dat) <- c("Symbol1", "Symbol2", "Title", "Evidence")
for (i in 1:nrow(dat)) {
title <- dat$Title[i]
dat$Title[i] <- paste("https://www.ncbi.nlm.nih.gov/pubmed",
'?term=(', dat$Title[i],'%5BTitle%5D',
')', sep='')
dat$Title[i] <- paste('<a href="', dat$Title[i], '" target="_blank">', title,
'</a>', sep="")
dat$Title[i] <- HTML(dat$Title[i])
}
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
#### RAPdb
fetchInfoByRap <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.rap.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
gene.fl <- paste(path, "gene.info", sep="/")
if (file.exists(gene.fl)) {
dat <- read.table(gene.fl, head=T, sep="\t", as.is=T)
msu <- unlist(strsplit(dat$MSU, split='|', fixed=TRUE))
msu.new <- sapply(msu, function(x){
if (x!="None") {
y <- paste("http://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
msu.new <- paste(unname(msu.new), sep="", collapse="|")
dat$MSU <- msu.new
rap <- unlist(strsplit(dat$RAPdb, split='|', fixed=TRUE))
rap.new <- sapply(rap, function(x){
if (x!="None") {
y <- paste("https://rapdb.dna.affrc.go.jp/locus/?name=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
rap.new <- paste(unname(rap.new), sep="", collapse="|")
dat$RAPdb <- rap.new
return(dat)
}
} else {
return(NULL)
}
}
fetchFamInfoByRap <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- fam.gene.rap.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
dat <- fam.gene.info[locus.line, ]
msu <- unlist(strsplit(dat$MSU, split='|', fixed=TRUE))
msu.new <- sapply(msu, function(x){
if (x!="None") {
y <- paste("http://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
msu.new <- paste(unname(msu.new), sep="", collapse="|")
dat$MSU <- msu.new
rap <- unlist(strsplit(dat$RAPdb, split='|', fixed=TRUE))
rap.new <- sapply(rap, function(x){
if (x!="None") {
y <- paste("https://rapdb.dna.affrc.go.jp/locus/?name=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
rap.new <- paste(unname(rap.new), sep="", collapse="|")
dat$RAPdb <- rap.new
dat$path <- NULL
return(dat)
} else {
return(NULL)
}
}
fetchRefByRap <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.rap.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
ref.fl <- paste(path, "reference.info", sep="/")
if (file.exists(ref.fl)) {
dat <- read.table(ref.fl, head=T, sep="\t", as.is=T,
quote="", comment="")
dat$Publication <- NULL
dat$Affiliation <- NULL
for (i in 1:nrow(dat)) {
title <- dat$Title[i]
dat$Title[i] <- paste("https://www.ncbi.nlm.nih.gov/pubmed",
'?term=(', dat$Title[i],'%5BTitle%5D',
')', sep='')
dat$Title[i] <- paste('<a href="', dat$Title[i], '" target="_blank">', title,
'</a>', sep="")
dat$Title[i] <- HTML(dat$Title[i])
}
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
fetchFamRefByRap <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- fam.gene.rap.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- fam.gene.info$path[locus.line]
ref.fl <- paste(path, "family.ref", sep="/")
if (file.exists(ref.fl)) {
dat <- read.table(ref.fl, head=T, sep="\t", as.is=T,
quote="", comment="")
dat$Affiliation <- NULL
for (i in 1:nrow(dat)) {
title <- dat$Title[i]
dat$Title[i] <- paste("https://www.ncbi.nlm.nih.gov/pubmed",
'?term=(', dat$Title[i],'%5BTitle%5D',
')', sep='')
dat$Title[i] <- paste('<a href="', dat$Title[i], '" target="_blank">', title,
'</a>', sep="")
dat$Title[i] <- HTML(dat$Title[i])
}
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
fetchAccByRap <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.rap.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
acc.fls <- list.files(path, patter="*acc-*", full=T)
if (length(acc.fls)>0) {
acc.fls <- gsub(".+-", "", acc.fls)
acc.fls <- sapply(acc.fls, function(x){
y <- paste("https://www.ncbi.nlm.nih.gov/nuccore/", x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
})
dat <- data.frame(Accession=acc.fls, stringsAsFactors=FALSE)
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
fetchExpByRap <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.rap.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
exp.fl <- paste(path, "expression.info", sep="/")
if (file.exists(exp.fl)) {
dat <- read.table(exp.fl, head=T, sep="\t", as.is=T)
return(dat)
}
} else {
return(NULL)
}
}
fetchTextByRap <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.rap.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
text.fls <- list.files(path, patter="^pub.text.mining$", full=T)
if (length(text.fls)>0) {
text.con <- readLines(text.fls)
text.con <- text.con[!grepl("^symbol:", text.con)]
clone <- sapply(seq(2, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^cloning:\\s+", "", y)
return(y)
})
tdna <- sapply(seq(4, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^tdna:\\s+", "", y)
return(y)
})
tos <- sapply(seq(5, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^tos:\\s+", "", y)
return(y)
})
homo <- sapply(seq(6, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^homol:\\s+", "", y)
return(y)
})
rnai <- sapply(seq(7, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^rnai:\\s+", "", y)
return(y)
})
ove <- sapply(seq(8, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^ove:\\s+", "", y)
return(y)
})
rt <- sapply(seq(9, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^rt:\\s+", "", y)
return(y)
})
north <- sapply(seq(10, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^N:\\s+", "", y)
return(y)
})
south <- sapply(seq(11, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^S:\\s+", "", y)
return(y)
})
west <- sapply(seq(12, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^W:\\s+", "", y)
return(y)
})
access <- sapply(seq(3, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^access:\\s+", "", y)
return(y)
})
locus <- sapply(seq(1, length(text.con), by=12), function(x){
y <- text.con[x]
y <- gsub("^locus:\\s+", "", y)
return(y)
})
dat <- data.frame(Cloning=clone, TDNA=tdna, Tos17=tos, Homolog=homo,
RNAi=rnai, Overexp=ove, RTPCR=rt, Northern=north,
Southern=south, Western=west, Locus=locus,
Accession=access,
stringsAsFactors=FALSE)
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
fetchKeyByRap <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.rap.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
key.fl <- paste(path, "Keyword.trait", sep="/")
if (file.exists(key.fl)) {
dat <- read.table(key.fl, head=T, sep="\t", as.is=T,
quote="", comment="")
for (i in 1:nrow(dat)) {
title <- dat$Title[i]
dat$Title[i] <- paste("https://www.ncbi.nlm.nih.gov/pubmed",
'?term=(', dat$Title[i],'%5BTitle%5D',
')', sep='')
dat$Title[i] <- paste('<a href="', dat$Title[i], '" target="_blank">', title,
'</a>', sep="")
dat$Title[i] <- HTML(dat$Title[i])
}
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
fetchConneByRap <- function(locus="") {
locus <- gsub("^\\s+", "", locus)
locus <- gsub(" +$", "", locus)
locus.line <- gene.rap.final[locus]
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
conne.fl <- paste(path, "Connection", sep="/")
if (file.exists(conne.fl)) {
dat <- read.table(conne.fl, head=F, sep="\t", as.is=T,
quote="", comment="")
names(dat) <- c("Symbol1", "Symbol2", "Title", "Evidence")
for (i in 1:nrow(dat)) {
title <- dat$Title[i]
dat$Title[i] <- paste("https://www.ncbi.nlm.nih.gov/pubmed",
'?term=(', dat$Title[i],'%5BTitle%5D',
')', sep='')
dat$Title[i] <- paste('<a href="', dat$Title[i], '" target="_blank">', title,
'</a>', sep="")
dat$Title[i] <- HTML(dat$Title[i])
}
return(dat)
} else {
return(NULL)
}
} else {
return(NULL)
}
}
findDirBySym <- function(symbol="") {
line.tar <- sapply(1:nrow(gene.info), function(x){
sym.line <- gene.info$Symbol[x]
sym.line <- unlist(strsplit(sym.line, split='|', fixed=TRUE))
sym.line <- tolower(sym.line)
if (any(sym.line==symbol)) {
return(x)
} else {
return(NULL)
}
})
return(unlist(unname(line.tar)))
}
findDirByFamSym <- function(symbol="") {
line.tar <- sapply(1:nrow(fam.gene.info), function(x){
sym.line <- fam.gene.info$Symbol[x]
sym.line <- unlist(strsplit(sym.line, split='|', fixed=TRUE))
sym.line <- tolower(sym.line)
if (any(sym.line==symbol)) {
return(x)
} else {
return(NULL)
}
})
return(unlist(unname(line.tar)))
}
#### Symbol
fetchInfoBySym <- function(symbol="") {
symbol <- gsub("^\\s+", "", symbol)
symbol <- gsub(" +$", "", symbol)
locus.line <- findDirBySym(tolower(symbol))
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
gene.fl <- paste(path, "gene.info", sep="/")
if (file.exists(gene.fl)) {
dat <- read.table(gene.fl, head=T, sep="\t", as.is=T)
msu <- unlist(strsplit(dat$MSU, split='|', fixed=TRUE))
msu.new <- sapply(msu, function(x){
if (x!="None") {
y <- paste("http://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
msu.new <- paste(unname(msu.new), sep="", collapse="|")
dat$MSU <- msu.new
rap <- unlist(strsplit(dat$RAPdb, split='|', fixed=TRUE))
rap.new <- sapply(rap, function(x){
if (x!="None") {
y <- paste("https://rapdb.dna.affrc.go.jp/locus/?name=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
rap.new <- paste(unname(rap.new), sep="", collapse="|")
dat$RAPdb <- rap.new
return(dat)
}
} else if (length(locus.line)>1) {
dat <- gene.info[locus.line, ]
dat$path <- NULL
for (i in 1:nrow(dat)) {
msu <- unlist(strsplit(dat$MSU[i], split='|', fixed=TRUE))
msu.new <- sapply(msu, function(x){
if (x!="None") {
y <- paste("http://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
msu.new <- paste(unname(msu.new), sep="", collapse="|")
dat$MSU[i] <- msu.new
rap <- unlist(strsplit(dat$RAPdb[i], split='|', fixed=TRUE))
rap.new <- sapply(rap, function(x){
if (x!="None") {
y <- paste("https://rapdb.dna.affrc.go.jp/locus/?name=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
rap.new <- paste(unname(rap.new), sep="", collapse="|")
dat$RAPdb[i] <- rap.new
}
return(dat)
} else {
return(NULL)
}
}
fetchFamInfoBySym <- function(symbol="") {
symbol <- gsub("^\\s+", "", symbol)
symbol <- gsub(" +$", "", symbol)
locus.line <- findDirByFamSym(tolower(symbol))
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
dat <- fam.gene.info[locus.line, ]
dat$path <- NULL
for (i in 1:nrow(dat)) {
msu <- unlist(strsplit(dat$MSU[i], split='|', fixed=TRUE))
msu.new <- sapply(msu, function(x){
if (x!="None") {
y <- paste("http://rice.uga.edu/cgi-bin/ORF_infopage.cgi?orf=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
msu.new <- paste(unname(msu.new), sep="", collapse="|")
dat$MSU[i] <- msu.new
rap <- unlist(strsplit(dat$RAPdb[i], split='|', fixed=TRUE))
rap.new <- sapply(rap, function(x){
if (x!="None") {
y <- paste("https://rapdb.dna.affrc.go.jp/locus/?name=",
x, sep="")
y <- paste('<a href="', y, '" target="_blank">', x, '</a>', sep="")
y <- HTML(y)
return(y)
} else {
return("None")
}
})
rap.new <- paste(unname(rap.new), sep="", collapse="|")
dat$RAPdb[i] <- rap.new
}
return(dat)
} else {
return(NULL)
}
}
fetchRefBySym <- function(symbol="") {
symbol <- gsub("^\\s+", "", symbol)
symbol <- gsub(" +$", "", symbol)
locus.line <- findDirBySym(tolower(symbol))
if ( (length(locus.line)==1) && !is.na(locus.line) ) {
path <- gene.info$path[locus.line]
ref.fl <- paste(path, "reference.info", sep="/")
if (file.exists(ref.fl)) {
dat <- read.table(ref.fl, head=T, sep="\t", as.is=T,
quote="", comment="")
dat$Publication <- NULL
dat$Affiliation <- NULL