Score:-3

Ubuntu

How to sort the rows of a file as a matrix?

The_Bioinformatic_BATMAN

11/2/22, 2:36 PM

I would like to know how I can sort the rows of a file in the following way:

My file is file.txt (tab delimited):

g1 00A98_01563 00554_01552 CCUG38_01373 
g2 00554_01444
g3 00A98_04566 CCUG38_05322

I want to get this (tab delimited):

g 00A98 00554 CCUG38
g1 1 1 1
g2 0 1 0
g3 1 0 1

And/or also in this format (tab delimited):

g 00A98 00554 CCUG38
g1 00A98_01563 00554_01552 CCUG38_01373 
g2             00554_01444 
g3 00A98_04566             CCUG38_05322

How can I do it with the command line with sort, awk, grep or another?

All the best, Regards

2 + 3

command-line

text-processing

24601

11/2/22, 2:39 PM

read [ask] and [edit] your question with informtion on what you have tried and how this relates to ubuntu. Looks surprising like a homework question

Rinzwind

11/2/22, 2:50 PM

what you want is a feature of spreadsheets. So https://www.google.com/sheets/about/ or libreoffice would be the tool to use.

The_Bioinformatic_BATMAN

11/2/22, 3:53 PM

Listed, edited!

Score:4

Ubuntu

steeldriver

11/2/22, 6:10 PM

Using Miller, treat the input as delimit key-value pairs with TAB as the input field separator and underscore as the input pair separator, and set the output to TSV. Then you can unsparsify your data

$ mlr --idkvp --ifs tab --ips '_' --otsv unsparsify file.txt
1       00A98   00554   CCUG38
g1      01563   01552   01373
g2              01444
g3      04566           05322

You can then add various transformations ex.

$ mlr --idkvp --ifs tab --ips '_' --otsv unsparsify --fill-with 0 then put '
    for(k,v in mapexcept($*,"1")){if(v != 0){$[k] = 1}}
  ' then rename "1","g" file.txt
g       00A98   00554   CCUG38
g1      1       1       1
g2      0       1       0
g3      1       0       1

$ mlr --idkvp --ifs tab --ips '_' --otsv unsparsify then put -S '
    for(k,v in mapexcept($*,"1")){if(v != ""){$[k] = k ."_". v}}
  ' then rename "1","g" file.txt
g       00A98   00554   CCUG38
g1      00A98_01563     00554_01552     CCUG38_01373
g2              00554_01444
g3      00A98_04566             CCUG38_05322

The alignment looks "off" in the last case, but outputting with --ocsv in place of --tsv should confirm it is correct.

0 + 1

The_Bioinformatic_BATMAN

11/2/22, 8:54 PM

thanks a lot bro! you saved me a headache!

Score:2

Ubuntu

glenn jackman

11/2/22, 8:06 PM

This is toMatrix.awk

#!/usr/bin/env gawk -f
BEGIN { FS = OFS = "\t" }

{
    for (i=2; i<=NF; i++) {
        x=$i
        sub(/_.*/, "", x)
        if (!(x in values)) {
            values[x] = 1
            ordered[++value] = x
        }
        g[NR] = $1
        data[NR][x]=1
    }
}

END {
    printf "%s", "g"
    for (i = 1; i <= value; i++)
        printf "%s%s", OFS, ordered[i]
    print ""

    for (nr = 1; nr <= NR; nr++) {
        printf "%s", g[nr]
        for (i = 1; i <= value; i++)
            printf "%s%s", OFS, 0 + data[nr][ordered[i]]
        print ""
    }
}

$ gawk -f toMatrix.awk file.txt
g   00A98   00554   CCUG38
g1  1   1   1
g2  0   1   0
g3  1   0   1

0 + 1

The_Bioinformatic_BATMAN

11/2/22, 8:54 PM