MultiJoin (version 0.1.1)

FullJoin: create command to fully join multiple (more than 2) files

Description

Iteratively calls the function FullJoinPairs() to join lines of two files on a common field

Usage

FullJoin(files = c("ftr1.txt", "ftr2.txt"), prefix = " time ", 

    suffix = " > joined.txt", myjoin = FullJoinPairs, NumFields = rep(2, 

        length(files)), sep = c(" ", ",", "\t", "|")[1], mycat = c("", 

        "gunzip -cf ", "cat ")[1], filterStr = "", ReturnData = FALSE, 

    verbose = 2, ...)

Arguments

files

which files to join

prefix

any convenience prefix command to be passed to the beginning of the Unix command to be executed

suffix

any convenience suffix command to be passed to the end of the Unix command to be executed

myjoin

the particular Join function from the package to use

NumFields

this includes the userid column

sep

column delimiter; default white space

mycat

effective cat command, if empty do NOT use FIFos

filterStr

various inline filters that act locally and do not need an input file,

ReturnData

should the result of the join command be read into R and returned as a dataframe?

verbose

level of verbosity

…

further arguments to myjoin such as missingValue or extraARGS

Value

returns command only

Examples

# NOT RUN {

if (0){


  #no FIFOs:


  FullJoin(NumFields = rep(4,2))


  FullJoin(paste0("ftr",1:4,".txt"), NumFields = rep(4, 4), suffix = " | gzip > joined.txt.gz")


  FullJoin(paste0("ftr",1:4,".txt"), NumFields = rep(3, 4),missingValue="0", suffix = "")


  #with FIFOs:


  FullJoin(paste0("ftr",1:4,".txt"), mycat = "cat ", NumFields = rep(3, 4),missingValue="0", 


           suffix = "", verbose=2)


  FullJoin(paste0("ftr",1:3,".txt.gz"), mycat = "gunzip -cf ", filterStr = " | cut -f1,3", 


           NumFields = rep(2, 3), verbose=2)


  #selected columns only:


  FullJoin(paste0("ftr",1:3,".txt"), mycat = "cat ", filterStr = "cut -f1,3",  


           NumFields = rep(2, 3),missingValue="0", suffix = "", verbose=2)


  


  ret = ArtificialData(fakeDataDir="./fakeData2", joinKey=letters, numFiles = 10, 


                       N = rep(18,10), NCOL=rep(5,10))


  FullJoin(paste0("./fakeData2/file",1:10,".txt"),missingValue="0", suffix = "", verbose=2)


  


  # let's try FIFOs:


  #small:


  cmd = FullJoin(paste0("file",1:2,".txt"), mycat = "cat ", NumFields = rep(5, 2),


                 missingValue="0", suffix = " > joined.txt", verbose=2)


  


  cmd = FullJoin(paste0("file",1:3,".txt"), mycat = "cat ", NumFields = rep(5, 3),


                 missingValue="0", suffix = " > joined.txt", verbose=2)


  


  # and now gzipped files:


  ret = ArtificialData(fakeDataDir="./fakeData", joinKey=letters, numFiles = 10,GZIP =1, 


                       N = rep(18,10), NCOL=rep(5,10))


  cmd = FullJoin(paste0("./fakeData/file",1:10,".txt.gz"), mycat = "gunzip -c ",  


                 NumFields = rep(3, 10),missingValue="NA",


                 filterStr = " | cut -f1,2,3",


                 suffix = "  > joined.txt", verbose=2)


  


  x = FullJoin(paste0("./fakeData/file",1:10,".txt.gz"), mycat = "gunzip -c ",  


               NumFields = rep(3, 10),missingValue="NA",


               filterStr = " | cut -f1,2,3",ReturnData=TRUE,


               suffix = "", verbose=0)


}


#let us try a laarge example





#uids = sort(paste0(sample(LETTERS,10^7,replace=TRUE), sample(10^8,10^7)))


#uids = paste0(LETTERS, (10^7):(10^8))


#tmp=expand.grid(LETTERS,LETTERS,LETTERS,0:9,0:9);str(tmp)


#uids=apply(expand.grid(LETTERS[1:3],LETTERS[1:3],0:2,0:3),1,paste0,collapse="")


#uids=apply(expand.grid(LETTERS,LETTERS,LETTERS,0:9,0:9),1,paste0,collapse="")


if (0) {


  uids = scan("uids.txt",what="")


  Nfiles=100          


  ret = ArtificialData(fakeDataDir="./fakeData", joinKey=uids, 


                 numFiles = Nfiles, GZIP =1, N = rep(10^5,Nfiles), NCOL=rep(10,Nfiles))


  cmd = FullJoin(paste0("fakeData/file",1:10,".txt.gz"), mycat = "gunzip -c ",  


                 NumFields = rep(3, 10),missingValue="NA",


                 filterStr = " | cut -f1,2,3",


                 suffix = " | gzip > ./fakeData/joined.txt.gz", verbose=2)


  system("rm /tmp/fifo*")


  for (go in cmd) system(go)


  


  x = FullJoin(paste0("./fakeData/file",1:10,".txt.gz"), mycat = "gunzip -c ",  


               NumFields = rep(3, 10),missingValue="NA",


               filterStr = " | cut -f1,2,3",ReturnData=TRUE,


               suffix = "", prefix="", verbose=0)


}





# }