Question

I’d like to transform a table in such a way that for duplicated
values in column #2 it would have corresponding values from column #1.

I.e. something like that…

MZ00024296  AC148152.3_FG005

MZ00047079  AC148152.3_FG006

MZ00028122  AC148152.3_FG008

MZ00032922  AC148152.3_FG008

MZ00048218  AC148152.3_FG008

MZ00024680  AC148167.6_FG001

MZ00013456  AC149475.2_FG003

to

AC148152.3_FG005    MZ00024296

AC148152.3_FG006    MZ00047079

AC148152.3_FG008    MZ00028122|MZ00032922|MZ00048218

AC148167.6_FG001 MZ00024680

AC149475.2_FG003 MZ00013456

As I need it to computations in R I tried to use:

x=aggregate(mz_grmz,by=list(mz_grmz[,2]),FUN=paste(mz_grmz[,1],sep="|"))

but it don’t work (wrong function)
Error in match.fun(FUN) :
‘paste(mz_grmz[, 1], sep = “|”)’ is not a function, character or symbol

I also remind myself about unstack() function, but it isn’t what I need.

I tried to do it using awk, based on my base knowledge I reworked code given here:

site1

#! /bin/sh
for y do
awk -v FS="\t" '{
for (x=1;x<=NR;x++) {
    if (NR>2 && x=x+1) {
    print $2"\t"x
    }
    else {print NR}
}
}' $y > $y.2
done

unfortunately it doesn’t work, it’s only produce enormous file with field #2 and some numbers.

I suppose it is easy task, but it is above my skills right now.
Could somebody give me a hint? Maybe just function to use in aggregate in R.

Thanks

Answer 1

You could do it in awk like this:

awk '
    {
        if ($2 in a)
            a[$2] = a[$2] "|" $1
        else
            a[$2] = $1
    }
    END {
        for (i in a)
            print i, a[i]
    }' INFILE > OUTFILE