R/KingMed_Abnormal_immunoglobulin.R
In yikeshu0611/KingMedRTools: What the Package Does (One Line, Title Case)
#' To clear immunoglobulin data from King Med test to a dataframe
#'
#' @param filename the name of fusion gene data text
#' @param WriteExecl A logical object. TRUE as default to write excel
#'
#' @return a dataframe
#' @export
#'
#' @examples KingMed_Abnormal_immunoglobulin("data.txt")
KingMed_Abnormal_immunoglobulin<-function(filename,WriteExecl=TRUE){
{
library(textreadr)
library(stringr)
library(stringi)
library(magrittr)
library(plyr)
library(tmcn)
}
#read the long string
if (grepl(".txt",filename)) { TRdata=suppressWarnings(toString(readLines(filename)))
}else if(grepl(".doc",filename) | grepl(".docx",filename)) {TRdata=toString(read_docx(filename))}
#standardize characters
TRdata=stri_trans_nfkd(TRdata)
TRdata=TRdata %>%
gsub(pattern = toUTF8("\u533B \u9662"),replacement = toUTF8("\u533B\u9662"))%>%
gsub(pattern = toUTF8("\u79D1 \u5BA4"),replacement = toUTF8("\u79D1\u5BA4"))%>%
gsub(pattern = toUTF8("\u6027 \u522B"),replacement = toUTF8("\u6027\u522B"))%>%
gsub(pattern = toUTF8("\u5E74 \u9F84"),replacement = toUTF8("\u5E74\u9F84"))%>%
gsub(pattern = toUTF8("CD45\u5F31, \u8868\u8FBE\u7EC6\u80DE"),replacement = toUTF8("CD45\u5F31\u8868\u8FBE\u7EC6\u80DE"))%>%
gsub(pattern = toUTF8("CD45\u9634\u6027, \u8868\u8FBE\u7EC6\u80DE"),replacement = toUTF8("CD45\u9634\u6027\u8868\u8FBE\u7EC6\u80DE"))%>%
gsub(pattern = toUTF8("\u5355\u6838\u7EC6, \u80DE"),replacement = toUTF8("\u5355\u6838\u7EC6\u80DE"))%>%
gsub(pattern = toUTF8("\u7EFC, \u5408\u8003\u8651"),replacement = toUTF8("\u7EFC\u5408\u8003\u8651"))%>%
gsub(pattern = toUTF8("\u5F62, \u6001\u5B66"),replacement = toUTF8("\u5F62\u6001\u5B66"))%>%
gsub(pattern = toUTF8("\u5176, \u514D\u75AB\u8868\u578B"),replacement = toUTF8("\u5176\u514D\u75AB\u8868\u578B"))%>%
gsub(pattern = toUTF8("\u8F85, \u52A9\u8BCA\u65AD\u65B9\u6CD5"),replacement = toUTF8("\u8F85\u52A9\u8BCA\u65AD\u65B9\u6CD5"))%>%
gsub(pattern = toUTF8("\u5176\u5B83, \u4E34\u5E8A\u4FE1\u606F"),replacement = toUTF8("\u5176\u5B83\u4E34\u5E8A\u4FE1\u606F"))%>%
gsub(pattern = toUTF8("\u59D3 \u540D"),replacement = toUTF8("\u59D3\u540D"))%>%
gsub(pattern = toUTF8(" \u8F7B\u94FE"),replacement = toUTF8("\u8F7B\u94FE"))%>%
gsub(pattern = toUTF8(" \u6E38\u79BB\u8F7B\u94FE"),replacement = toUTF8("\u6E38\u79BB\u8F7B\u94FE"))
#split
tongren=toUTF8('\u4E0A\u6D77\u4EA4\u901A\u5927\u5B66\u533B\u5B66\u9662\u9644\u5C5E\u540C\u4EC1\u533B\u9662')
TRdata1=strsplit(x = TRdata,split = tongren)[[1]]
#get purpose data
#abnormal immueglobal emia
Elp=toUTF8("\u7535\u6CF3\\(\u5957\u9910\u4E13\u7528\u9879\u76EE\\)")
AbIgLightChain=toUTF8("\u5F02\u5E38\u514D\u75AB\u7403\u86CB\u767D\u8840\u75C7\u8840\u6E05\u8F7B\u94FE")
dataget=c()
for (data.i in 1:length(TRdata1)) {
if ((grepl(Elp,TRdata1[data.i])|
grepl(AbIgLightChain,TRdata1[data.i]))){
dataget=c(dataget,data.i)
}
}
#extract abnormal ig data
dataget
length(dataget)
TRdata2=abnormalig=TRdata1[dataget]
#
TR.datafrme=data.frame()
prgbar<- txtProgressBar(min = 0, max = length(dataget),
style = 3,
initial = 0,width = 35)
for (flui.i in 1:length(dataget)) {
#page i
TRdata2.i=TRdata2[flui.i]
#Title
{
#sample code
SampleCode=toUTF8("\u6807\u672C\u6761\u7801")
SampleCode.Num=gsub(pattern = " ",replacement = "",
x=gsub(pattern = SampleCode,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(SampleCode,"[0-9a-zA-Z ]{1,}"))))
#PatientName
PatientName=toUTF8("\u75C5\u4EBA\u59D3\u540D")
PatientName.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = toUTF8("\u79D1\u5BA4"),replacement = "",
sub(pattern = toUTF8("\u59D3\u540D"),replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(toUTF8("\u59D3\u540D"),".*",toUTF8("\u79D1\u5BA4"))))))
#Department
Department=toUTF8("\u79D1\u5BA4")
Department.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = toUTF8("\u5B9E\u9A8C\u53F7"),replacement = "",
sub(pattern = Department,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(Department,".*",toUTF8("\u5B9E\u9A8C\u53F7"))))))
#sex
sex=toUTF8("\u6027\u522B")
sex.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = toUTF8("\u4F4F\u9662/\u95E8\u8BCA\u53F7"),replacement = "",
sub(pattern = sex,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(sex,".*",toUTF8("\u4F4F\u9662/\u95E8\u8BCA\u53F7"))))))
#bedid
bedid=toUTF8("\u623F/\u5E8A\u53F7")
bedid.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = toUTF8("\u6807\u672C\u60C5\u51B5"),replacement = "",
sub(pattern = bedid,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(bedid,".*",toUTF8("\u6807\u672C\u60C5\u51B5"))))))
if (substring(bedid.Num,1,1)=="+"){bedid.Num=sub(pattern = "\\+",replacement = "",
x = paste0(toUTF8("\u4E34"),bedid.Num))}
#Hospitalid
Hospitalid=toUTF8("\u95E8\u8BCA/\u4F4F\u9662\u53F7")
Hospitalid.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = paste0('[ ,]*',toUTF8("\u9001\u68C0\u6807\u672C")),replacement = "",
sub(pattern = toUTF8("\u4F4F\u9662/\u95E8\u8BCA\u53F7"),replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(toUTF8("\u4F4F\u9662/\u95E8\u8BCA\u53F7"),".*", toUTF8("\u9001\u68C0\u6807\u672C"))))))
#age
age=toUTF8("\u5E74\u9F84")
age.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = paste0('[ ,]*',toUTF8("\u623F/\u5E8A\u53F7")),replacement = "",
sub(pattern = age,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(age,".*", toUTF8("\u623F/\u5E8A\u53F7"))))))
#AcceptTime
AcceptTime=toUTF8('\u63A5\u6536\u65F6\u95F4')
AcceptTime.Num=sub(pattern = " ",replacement = "",
x=sub(pattern = paste0('[ ,]*',toUTF8("\u9879\u76EE \u68C0\u6D4B\u65B9\u6CD5")),replacement = "",
sub(pattern = AcceptTime,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(AcceptTime,".*", toUTF8("\u9879\u76EE \u68C0\u6D4B\u65B9\u6CD5"))))))
#ApplyDoctor
ApplyDoctor=toUTF8("\u7533\u8BF7\u533B\u751F")
ApplyDoctor.Num=sub(pattern = " ",replacement = "",
x=sub(pattern = paste0('[ ,]*',toUTF8("\u91C7\u6837\u65F6\u95F4")),replacement = "",
sub(pattern = ApplyDoctor,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(ApplyDoctor,".*", toUTF8("\u91C7\u6837\u65F6\u95F4"))))))
#bacterial
bacterial=toUTF8("\u9001\u68C0\u6750\u6599")
bacterial.Num=sub(pattern = " ",replacement = "",
x=sub(pattern = paste0('[ ,]*',age),replacement = "",
sub(pattern = toUTF8("\u9001\u68C0\u6807\u672C"),replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(toUTF8("\u9001\u68C0\u6807\u672C"),".*", age)))))
#SamplingTime
SamplingTime=toUTF8("\u91C7\u6837\u65F6\u95F4")
SamplingTime.Num=gsub(pattern = '[a-zA-Z ,]*',replacement = "",
sub(pattern = toUTF8("\u91C7\u6837\u65F6\u95F4"),replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(toUTF8("\u91C7\u6837\u65F6\u95F4"),"[a-zA-Z0-9- ]*"))))
}
{
#get data frame
first_title_location=c()
last_title_location=c()
first_title_location=max(gregexpr(Elp,TRdata2.i)[[1]][1],
gregexpr(AbIgLightChain,TRdata2.i)[[1]][1])
last_title_location=max(gregexpr(toUTF8("\u5EFA\u8BAE\u4E0E\u89E3\u91CA:"),TRdata2.i)[[1]][1],
gregexpr(toUTF8("\u68C0\u6D4B\u8BBE\u5907:"),TRdata2.i)[[1]][1])
DataFrame=substring(TRdata2.i,first_title_location,last_title_location-1)%>%
gsub(pattern = paste0(" ","\\S*",toUTF8("\u6cd5")," "),replacement = ";")%>%
gsub(pattern = " ",replacement = ";")%>%
sub(pattern = Elp,replacement = "")%>%
sub(pattern = AbIgLightChain,replacement = "")%>%
sub(pattern = toUTF8("\u8840\u6E05\u86CB\u767D\u5B9A\u91CF\u7EC4\u5408"),replacement = "")%>%
gsub(pattern = ",;",replacement = ",")%>%
gsub(pattern = ";%",replacement = "%")%>%
gsub(pattern = ",{0,1}fr_flag,{0,1}",replacement = "")%>%
sub(pattern = paste0("SP;G;A;M;",".*"),replacement = "")
DataFramelist=strsplit(x = DataFrame,split = ",")
#in order to delet space list unit
deletn=c()
for (j in 1:length(DataFramelist[[1]])) {
if (nchar(DataFramelist[[1]][j])==0){
deletn=c(deletn,j)
}
}
if (length(deletn)>=1){
DataFramelist=DataFramelist[[1]][-deletn]
}
DataFramelist2=strsplit(x = DataFramelist,split = ";")
Results=c()
for (fgunlist.i in DataFramelist2) {
fgunlist.clear= fgunlist.i[2] %>%
sub(pattern = ".*\\(",replacement = "")%>%
sub(pattern = "\\)",replacement = "")
Results=c(Results,fgunlist.clear)
}
Results=ifelse(Results=="+",toUTF8("\u9633\u6027"),Results)
Iterm=c()
for (fgunlist.i in DataFramelist2) {
Iterm=c(Iterm,fgunlist.i[1])
}
Iterm=paste0(bacterial.Num,"-",Iterm)
dt2col=cbind(Iterm,Results)
if (grepl(toUTF8("\u53D1\u73B0M\u86CB\u767D\u6761\u5E26"),TRdata2.i)){
Iterm=toUTF8("M\u86CB\u767D%")
Results=str_extract_all(string = TRdata2.i,pattern = "M[0-9]{0,1}:{0,1}[0-9]*\\.[0-9]*%{0,1}")
dt2col=rbind(dt2col,cbind(Iterm,Results))
}
}
##########
#dataframe
TR.datafrme.i=c()
TR.datafrme.i=cbind(SampleCode.Num,
PatientName.Num,
Department.Num,
sex.Num,
bedid.Num,
Hospitalid.Num,
age.Num,
ApplyDoctor.Num,
SamplingTime.Num)
TR.datafrme.i=data.frame(matrix(rep(TR.datafrme.i,each=nrow(dt2col)),nrow = nrow(dt2col)))
colnames(TR.datafrme.i)= c(SampleCode,
PatientName,
Department,
sex,
bedid,
Hospitalid,
age,
ApplyDoctor,
SamplingTime)
TR.datafrme.bind=cbind(TR.datafrme.i,data.frame(dt2col))
TR.datafrme=rbind.fill(TR.datafrme,TR.datafrme.bind)
setTxtProgressBar(pb = prgbar, value = flui.i)
}
close(prgbar)
TR.datafrme1=tidyr::spread(unique(TR.datafrme),Iterm,Results)
TR.datafrme=data.frame(ifelse(is.na(as.matrix(TR.datafrme1)),"",as.matrix(TR.datafrme1)))
colnames(TR.datafrme)=colnames(TR.datafrme1)
cat( toUTF8("\u68C0\u6D4B\u9879\u76EE:"),
"\n",
toUTF8("\u8840\u6E05\u86CB\u767D\u5B9A\u91CF\u7EC4\u5408"),
"\n",
toUTF8("\u8840\u6E05\u86CB\u767D\u7535\u6CF3(\u5957\u9910\u4E13\u7528\u9879\u76EE)"),
"\n",
toUTF8("\u8840\u6E05\u514D\u75AB\u56FA\u5B9A\u7535\u6CF3(\u5957\u9910\u4E13\u7528\u9879\u76EE)"),
"\n",
toUTF8("\u5C3F\u672C\u5468\u6C0F\u86CB\u767D\u7535\u6CF3(\u5957\u9910\u4E13\u7528\u9879\u76EE)"),
"\n",
toUTF8("\u5C3F\u86CB\u767D\u7535\u6CF3(\u5957\u9910\u4E13\u7528\u9879\u76EE)"),
"\n",
toUTF8("\u5F02\u5E38\u514D\u75AB\u7403\u86CB\u767D\u8840\u75C7\u8840\u6E05\u8F7B\u94FE")
)
if (WriteExecl==TRUE){
filenamewritten=Sys.time() %>%
sub(pattern = ":",replacement = toUTF8("\u02B1"))%>%
sub(pattern = ":",replacement = toUTF8("\u5206"))%>%
paste0(toUTF8("\u79D2 \u5F02\u5E38\u514D\u75AB\u7403\u86CB\u767D.csv"))
write.csv(TR.datafrme,filenamewritten)
cat("\n","\n",
toUTF8("\u6570\u636E\u88AB\u5199\u5165Excel\u4E2D,\u6587\u4EF6\u540D\u4E3A:"),
"\n",
filenamewritten)
}
return(TR.datafrme)
}
yikeshu0611/KingMedRTools documentation built on May 11, 2019, 8:29 p.m.
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#' To clear immunoglobulin data from King Med test to a dataframe
#'
#' @param filename the name of fusion gene data text
#' @param WriteExecl A logical object. TRUE as default to write excel
#'
#' @return a dataframe
#' @export
#'
#' @examples KingMed_Abnormal_immunoglobulin("data.txt")
KingMed_Abnormal_immunoglobulin<-function(filename,WriteExecl=TRUE){
{
library(textreadr)
library(stringr)
library(stringi)
library(magrittr)
library(plyr)
library(tmcn)
}
#read the long string
if (grepl(".txt",filename)) { TRdata=suppressWarnings(toString(readLines(filename)))
}else if(grepl(".doc",filename) | grepl(".docx",filename)) {TRdata=toString(read_docx(filename))}
#standardize characters
TRdata=stri_trans_nfkd(TRdata)
TRdata=TRdata %>%
gsub(pattern = toUTF8("\u533B \u9662"),replacement = toUTF8("\u533B\u9662"))%>%
gsub(pattern = toUTF8("\u79D1 \u5BA4"),replacement = toUTF8("\u79D1\u5BA4"))%>%
gsub(pattern = toUTF8("\u6027 \u522B"),replacement = toUTF8("\u6027\u522B"))%>%
gsub(pattern = toUTF8("\u5E74 \u9F84"),replacement = toUTF8("\u5E74\u9F84"))%>%
gsub(pattern = toUTF8("CD45\u5F31, \u8868\u8FBE\u7EC6\u80DE"),replacement = toUTF8("CD45\u5F31\u8868\u8FBE\u7EC6\u80DE"))%>%
gsub(pattern = toUTF8("CD45\u9634\u6027, \u8868\u8FBE\u7EC6\u80DE"),replacement = toUTF8("CD45\u9634\u6027\u8868\u8FBE\u7EC6\u80DE"))%>%
gsub(pattern = toUTF8("\u5355\u6838\u7EC6, \u80DE"),replacement = toUTF8("\u5355\u6838\u7EC6\u80DE"))%>%
gsub(pattern = toUTF8("\u7EFC, \u5408\u8003\u8651"),replacement = toUTF8("\u7EFC\u5408\u8003\u8651"))%>%
gsub(pattern = toUTF8("\u5F62, \u6001\u5B66"),replacement = toUTF8("\u5F62\u6001\u5B66"))%>%
gsub(pattern = toUTF8("\u5176, \u514D\u75AB\u8868\u578B"),replacement = toUTF8("\u5176\u514D\u75AB\u8868\u578B"))%>%
gsub(pattern = toUTF8("\u8F85, \u52A9\u8BCA\u65AD\u65B9\u6CD5"),replacement = toUTF8("\u8F85\u52A9\u8BCA\u65AD\u65B9\u6CD5"))%>%
gsub(pattern = toUTF8("\u5176\u5B83, \u4E34\u5E8A\u4FE1\u606F"),replacement = toUTF8("\u5176\u5B83\u4E34\u5E8A\u4FE1\u606F"))%>%
gsub(pattern = toUTF8("\u59D3 \u540D"),replacement = toUTF8("\u59D3\u540D"))%>%
gsub(pattern = toUTF8(" \u8F7B\u94FE"),replacement = toUTF8("\u8F7B\u94FE"))%>%
gsub(pattern = toUTF8(" \u6E38\u79BB\u8F7B\u94FE"),replacement = toUTF8("\u6E38\u79BB\u8F7B\u94FE"))
#split
tongren=toUTF8('\u4E0A\u6D77\u4EA4\u901A\u5927\u5B66\u533B\u5B66\u9662\u9644\u5C5E\u540C\u4EC1\u533B\u9662')
TRdata1=strsplit(x = TRdata,split = tongren)[[1]]
#get purpose data
#abnormal immueglobal emia
Elp=toUTF8("\u7535\u6CF3\\(\u5957\u9910\u4E13\u7528\u9879\u76EE\\)")
AbIgLightChain=toUTF8("\u5F02\u5E38\u514D\u75AB\u7403\u86CB\u767D\u8840\u75C7\u8840\u6E05\u8F7B\u94FE")
dataget=c()
for (data.i in 1:length(TRdata1)) {
if ((grepl(Elp,TRdata1[data.i])|
grepl(AbIgLightChain,TRdata1[data.i]))){
dataget=c(dataget,data.i)
}
}
#extract abnormal ig data
dataget
length(dataget)
TRdata2=abnormalig=TRdata1[dataget]
#
TR.datafrme=data.frame()
prgbar<- txtProgressBar(min = 0, max = length(dataget),
style = 3,
initial = 0,width = 35)
for (flui.i in 1:length(dataget)) {
#page i
TRdata2.i=TRdata2[flui.i]
#Title
{
#sample code
SampleCode=toUTF8("\u6807\u672C\u6761\u7801")
SampleCode.Num=gsub(pattern = " ",replacement = "",
x=gsub(pattern = SampleCode,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(SampleCode,"[0-9a-zA-Z ]{1,}"))))
#PatientName
PatientName=toUTF8("\u75C5\u4EBA\u59D3\u540D")
PatientName.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = toUTF8("\u79D1\u5BA4"),replacement = "",
sub(pattern = toUTF8("\u59D3\u540D"),replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(toUTF8("\u59D3\u540D"),".*",toUTF8("\u79D1\u5BA4"))))))
#Department
Department=toUTF8("\u79D1\u5BA4")
Department.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = toUTF8("\u5B9E\u9A8C\u53F7"),replacement = "",
sub(pattern = Department,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(Department,".*",toUTF8("\u5B9E\u9A8C\u53F7"))))))
#sex
sex=toUTF8("\u6027\u522B")
sex.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = toUTF8("\u4F4F\u9662/\u95E8\u8BCA\u53F7"),replacement = "",
sub(pattern = sex,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(sex,".*",toUTF8("\u4F4F\u9662/\u95E8\u8BCA\u53F7"))))))
#bedid
bedid=toUTF8("\u623F/\u5E8A\u53F7")
bedid.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = toUTF8("\u6807\u672C\u60C5\u51B5"),replacement = "",
sub(pattern = bedid,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(bedid,".*",toUTF8("\u6807\u672C\u60C5\u51B5"))))))
if (substring(bedid.Num,1,1)=="+"){bedid.Num=sub(pattern = "\\+",replacement = "",
x = paste0(toUTF8("\u4E34"),bedid.Num))}
#Hospitalid
Hospitalid=toUTF8("\u95E8\u8BCA/\u4F4F\u9662\u53F7")
Hospitalid.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = paste0('[ ,]*',toUTF8("\u9001\u68C0\u6807\u672C")),replacement = "",
sub(pattern = toUTF8("\u4F4F\u9662/\u95E8\u8BCA\u53F7"),replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(toUTF8("\u4F4F\u9662/\u95E8\u8BCA\u53F7"),".*", toUTF8("\u9001\u68C0\u6807\u672C"))))))
#age
age=toUTF8("\u5E74\u9F84")
age.Num=gsub(pattern = " ",replacement = "",
x=sub(pattern = paste0('[ ,]*',toUTF8("\u623F/\u5E8A\u53F7")),replacement = "",
sub(pattern = age,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(age,".*", toUTF8("\u623F/\u5E8A\u53F7"))))))
#AcceptTime
AcceptTime=toUTF8('\u63A5\u6536\u65F6\u95F4')
AcceptTime.Num=sub(pattern = " ",replacement = "",
x=sub(pattern = paste0('[ ,]*',toUTF8("\u9879\u76EE \u68C0\u6D4B\u65B9\u6CD5")),replacement = "",
sub(pattern = AcceptTime,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(AcceptTime,".*", toUTF8("\u9879\u76EE \u68C0\u6D4B\u65B9\u6CD5"))))))
#ApplyDoctor
ApplyDoctor=toUTF8("\u7533\u8BF7\u533B\u751F")
ApplyDoctor.Num=sub(pattern = " ",replacement = "",
x=sub(pattern = paste0('[ ,]*',toUTF8("\u91C7\u6837\u65F6\u95F4")),replacement = "",
sub(pattern = ApplyDoctor,replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(ApplyDoctor,".*", toUTF8("\u91C7\u6837\u65F6\u95F4"))))))
#bacterial
bacterial=toUTF8("\u9001\u68C0\u6750\u6599")
bacterial.Num=sub(pattern = " ",replacement = "",
x=sub(pattern = paste0('[ ,]*',age),replacement = "",
sub(pattern = toUTF8("\u9001\u68C0\u6807\u672C"),replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(toUTF8("\u9001\u68C0\u6807\u672C"),".*", age)))))
#SamplingTime
SamplingTime=toUTF8("\u91C7\u6837\u65F6\u95F4")
SamplingTime.Num=gsub(pattern = '[a-zA-Z ,]*',replacement = "",
sub(pattern = toUTF8("\u91C7\u6837\u65F6\u95F4"),replacement = "",
x =str_extract(string = TRdata2.i,
pattern = paste0(toUTF8("\u91C7\u6837\u65F6\u95F4"),"[a-zA-Z0-9- ]*"))))
}
{
#get data frame
first_title_location=c()
last_title_location=c()
first_title_location=max(gregexpr(Elp,TRdata2.i)[[1]][1],
gregexpr(AbIgLightChain,TRdata2.i)[[1]][1])
last_title_location=max(gregexpr(toUTF8("\u5EFA\u8BAE\u4E0E\u89E3\u91CA:"),TRdata2.i)[[1]][1],
gregexpr(toUTF8("\u68C0\u6D4B\u8BBE\u5907:"),TRdata2.i)[[1]][1])
DataFrame=substring(TRdata2.i,first_title_location,last_title_location-1)%>%
gsub(pattern = paste0(" ","\\S*",toUTF8("\u6cd5")," "),replacement = ";")%>%
gsub(pattern = " ",replacement = ";")%>%
sub(pattern = Elp,replacement = "")%>%
sub(pattern = AbIgLightChain,replacement = "")%>%
sub(pattern = toUTF8("\u8840\u6E05\u86CB\u767D\u5B9A\u91CF\u7EC4\u5408"),replacement = "")%>%
gsub(pattern = ",;",replacement = ",")%>%
gsub(pattern = ";%",replacement = "%")%>%
gsub(pattern = ",{0,1}fr_flag,{0,1}",replacement = "")%>%
sub(pattern = paste0("SP;G;A;M;",".*"),replacement = "")
DataFramelist=strsplit(x = DataFrame,split = ",")
#in order to delet space list unit
deletn=c()
for (j in 1:length(DataFramelist[[1]])) {
if (nchar(DataFramelist[[1]][j])==0){
deletn=c(deletn,j)
}
}
if (length(deletn)>=1){
DataFramelist=DataFramelist[[1]][-deletn]
}
DataFramelist2=strsplit(x = DataFramelist,split = ";")
Results=c()
for (fgunlist.i in DataFramelist2) {
fgunlist.clear= fgunlist.i[2] %>%
sub(pattern = ".*\\(",replacement = "")%>%
sub(pattern = "\\)",replacement = "")
Results=c(Results,fgunlist.clear)
}
Results=ifelse(Results=="+",toUTF8("\u9633\u6027"),Results)
Iterm=c()
for (fgunlist.i in DataFramelist2) {
Iterm=c(Iterm,fgunlist.i[1])
}
Iterm=paste0(bacterial.Num,"-",Iterm)
dt2col=cbind(Iterm,Results)
if (grepl(toUTF8("\u53D1\u73B0M\u86CB\u767D\u6761\u5E26"),TRdata2.i)){
Iterm=toUTF8("M\u86CB\u767D%")
Results=str_extract_all(string = TRdata2.i,pattern = "M[0-9]{0,1}:{0,1}[0-9]*\\.[0-9]*%{0,1}")
dt2col=rbind(dt2col,cbind(Iterm,Results))
}
}
##########
#dataframe
TR.datafrme.i=c()
TR.datafrme.i=cbind(SampleCode.Num,
PatientName.Num,
Department.Num,
sex.Num,
bedid.Num,
Hospitalid.Num,
age.Num,
ApplyDoctor.Num,
SamplingTime.Num)
TR.datafrme.i=data.frame(matrix(rep(TR.datafrme.i,each=nrow(dt2col)),nrow = nrow(dt2col)))
colnames(TR.datafrme.i)= c(SampleCode,
PatientName,
Department,
sex,
bedid,
Hospitalid,
age,
ApplyDoctor,
SamplingTime)
TR.datafrme.bind=cbind(TR.datafrme.i,data.frame(dt2col))
TR.datafrme=rbind.fill(TR.datafrme,TR.datafrme.bind)
setTxtProgressBar(pb = prgbar, value = flui.i)
}
close(prgbar)
TR.datafrme1=tidyr::spread(unique(TR.datafrme),Iterm,Results)
TR.datafrme=data.frame(ifelse(is.na(as.matrix(TR.datafrme1)),"",as.matrix(TR.datafrme1)))
colnames(TR.datafrme)=colnames(TR.datafrme1)
cat( toUTF8("\u68C0\u6D4B\u9879\u76EE:"),
"\n",
toUTF8("\u8840\u6E05\u86CB\u767D\u5B9A\u91CF\u7EC4\u5408"),
"\n",
toUTF8("\u8840\u6E05\u86CB\u767D\u7535\u6CF3(\u5957\u9910\u4E13\u7528\u9879\u76EE)"),
"\n",
toUTF8("\u8840\u6E05\u514D\u75AB\u56FA\u5B9A\u7535\u6CF3(\u5957\u9910\u4E13\u7528\u9879\u76EE)"),
"\n",
toUTF8("\u5C3F\u672C\u5468\u6C0F\u86CB\u767D\u7535\u6CF3(\u5957\u9910\u4E13\u7528\u9879\u76EE)"),
"\n",
toUTF8("\u5C3F\u86CB\u767D\u7535\u6CF3(\u5957\u9910\u4E13\u7528\u9879\u76EE)"),
"\n",
toUTF8("\u5F02\u5E38\u514D\u75AB\u7403\u86CB\u767D\u8840\u75C7\u8840\u6E05\u8F7B\u94FE")
)
if (WriteExecl==TRUE){
filenamewritten=Sys.time() %>%
sub(pattern = ":",replacement = toUTF8("\u02B1"))%>%
sub(pattern = ":",replacement = toUTF8("\u5206"))%>%
paste0(toUTF8("\u79D2 \u5F02\u5E38\u514D\u75AB\u7403\u86CB\u767D.csv"))
write.csv(TR.datafrme,filenamewritten)
cat("\n","\n",
toUTF8("\u6570\u636E\u88AB\u5199\u5165Excel\u4E2D,\u6587\u4EF6\u540D\u4E3A:"),
"\n",
filenamewritten)
}
return(TR.datafrme)
}
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