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Top Forums Shell Programming and Scripting Join multiple files by column with awk Post 302427249 by macsx82 on Friday 4th of June 2010 10:22:26 AM
Old 06-04-2010
Hi Ikki!
Thanks for your reply! I use awk bacause I'm more familiar with its sintax, i've just used sed a couple of time!
My files contain datas from genetic chips, and each file belongs to a person.
Each file has ~360000 lines.
You're right, I have more than one file shorter than the other..at the moment there are 95 shorter files. But they could increase, and yes, in shorter files it's possible that a line starting with cnvi0000004 is followed by a line starting with cnvi0000006 or cnvi0000008...it depends on how many records are missing for this person, but all input file are sorted by the first column.
As I said I've written an R-script that works, but it is extremely slow. In this script I compare a list of "complete" names with another and see if there are differences. Once i found elements that aren't in the short list, i add them in this list in order to have elements with same length. In this way I can merge all column and insert tabs instead of missing datas. I post the R-code:

Code:
#define file path
files_path="/home/###/###/people/"

#read all file names in the directory and save in a vector
only_files <- dir(path=files_path, pattern = "*.in") 
files = paste(files_path,only_files, sep="")

#load files to create the "complete list" I need the first column that contain the name of the record
tot_file <- read.table(files[1], sep="\t", header=TRUE)[c(1,2,3)]
tot_file_noname <- cbind(Chr=tot_file$Chr, Position=tot_file$Position)


for (i in 1:length(files)) { 
#
        xx_file <- read.table(files[i], sep="\t", header=TRUE)[c(1,3,4)]
        xx_file_noname <- cbind(xx_file$Position, xx_file$Log.R.Ratio)

#now I read each file and if i find some mismatch from the complete list 
#I add them in the current xx_file object with value "NaN"

    if (length(xx_file$name) != length(tot_file$name)){
                print('different!')
                mismatch=NULL

                match <- tot_file$name %in% xx_file$name
                                    
                for(i in 1:length(match)){ if (match[i]== FALSE){ mismatch = c(mismatch,i)}}

                missing_snp = NULL
# add missing values
                for (i in mismatch){
                    missing <- data.frame(Position = tot_file[i,]$Position, Log.R.Ratio="NaN")
                    missing_snp <- rbind(missing_snp, missing)
                }

                    xx_file_noname <- rbind(xx_file[,c(2,3)], missing_snp)
    }else{
        print('equals!')        
    }    

    tot_file_noname = cbind(tot_file_noname, xx_file_noname[,2])
}

# write the "big" file
write.table(tot_file_noname, file = "gigante.dat", append = FALSE, quote = FALSE, sep = "\t", eol = "\n", na = "NaN", dec =".", row.names = FALSE, col.names =TRUE)

Now I'm trying to port this in a shell script to have a faster response. My purpose was to avoid files preprocessing if i can, because of the large amount of data stored in each file, if possible.
I tried your command also, and it is running, the only problem is to add manually 1664 columns for the cut command, but I think I can work on It!
Hope I have been clear enough, and greatly appreciate your help!
 

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DIFF3(1)							     GNU Tools								  DIFF3(1)

NAME
diff3 - find differences between three files SYNOPSIS
diff3 [options] mine older yours DESCRIPTION
The diff3 command compares three files and outputs descriptions of their differences. The files to compare are mine, older, and yours. At most one of these three file names may be -, which tells diff3 to read the standard input for that file. Options Below is a summary of all of the options that GNU diff3 accepts. Multiple single letter options (unless they take an argument) can be com- bined into a single command line argument. -a Treat all files as text and compare them line-by-line, even if they do not appear to be text. -A Incorporate all changes from older to yours into mine, surrounding all conflicts with bracket lines. -B Old behavior of -A. Shows non-conflicts. -e Generate an ed script that incorporates all the changes from older to yours into mine. -E Like -e, except bracket lines from overlapping changes' first and third files. With -e, an overlapping change looks like this: <<<<<<< mine lines from mine ======= lines from yours >>>>>>> yours --ed Generate an ed script that incorporates all the changes from older to yours into mine. --easy-only Like -e, except output only the nonoverlapping changes. -i Generate w and q commands at the end of the ed script for System V compatibility. This option must be combined with one of the -AeExX3 options, and may not be combined with -m. --initial-tab Output a tab rather than two spaces before the text of a line in normal format. This causes the alignment of tabs in the line to look normal. -L label --label=label Use the label label for the brackets output by the -A, -E and -X options. This option may be given up to three times, one for each input file. The default labels are the names of the input files. Thus diff3 -L X -L Y -L Z -m A B C acts like diff3 -m A B C , except that the output looks like it came from files named X, Y and Z rather than from files named A, B and C. -m --merge Apply the edit script to the first file and send the result to standard output. Unlike piping the output from diff3 to ed, this works even for binary files and incomplete lines. -A is assumed if no edit script option is specified. --overlap-only Like -e, except output only the overlapping changes. --show-all Incorporate all unmerged changes from older to yours into mine, surrounding all overlapping changes with bracket lines. --show-overlap Like -e, except bracket lines from overlapping changes' first and third files. -T Output a tab rather than two spaces before the text of a line in normal format. This causes the alignment of tabs in the line to look normal. --text Treat all files as text and compare them line-by-line, even if they do not appear to be text. -v --version Output the version number of diff3. -x Like -e, except output only the overlapping changes. -X Like -E, except output only the overlapping changes. In other words, like -x, except bracket changes as in -E. -3 Like -e, except output only the nonoverlapping changes. SEE ALSO
cmp(1), comm(1), diff(1), ed(1), patch(1), sdiff(1). DIAGNOSTICS
An exit status of 0 means diff3 was successful, 1 means some conflicts were found, and 2 means trouble. GNU Tools 22sep1993 DIFF3(1)
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