Question

I am not sure if I can do this purely with sed:

I am trying to rearrange lines like this

GF:001,GF:00012,GF:01223<TAB>XXR
GF:001,GF:00012,GF:01223,GF:0666<TAB>XXXR3

to

GF:001<TAB>XXR
GF:00012<TAB>XXR
GF:01223<TAB>XXR
GF:001<TAB>XXXR3
GF:00012<TAB>XXXR3
GF:01223<TAB>XXXR3
GF:0666<TAB>XXXR3

Anyone any hints? The cardinality of GF:XXXX is alternating as the length of GF:XXXX is.

I am stuck with sed -n '
'/\(XX.*\)$/' {
s/,/\t\1\n/
}' input but I cannot reference to the originally matched pattern in the first place. any ideas? cheers!

Update:
I think it is not possible to do this with just using sed. So I used perl to do this:

perl -e 'open(IN, "< file");
while (<IN>) {
    @a = split(/\t/);
    @gos = split(/,/, $a[0]);
    foreach (@gos) {
      print $_."\t".$a[1];
    }
close( IN );' > output

But if anyone knows a way to solve this just with sed please post it here…

Answer 1

It can be done in sed, though I probably would use Perl (or Awk or Python) to do it.

I claim no elegance for this solution, but brute force and ignorance sometimes pays off. I created a file called, unoriginally, sed.script containing:

/\(GF:[0-9]*\),\(.*\)<TAB>\(.*\)/{
:redo
s/\(GF:[0-9]*\),\(.*\)<TAB>\(.*\)/\1<TAB>\3@@@@@\2<TAB>\3/
h
s/@@@@@.*//
p
x
s/.*@@@@@//
t redo
d
}

I ran it as:

sed -f sed.script input

where input contained the two lines shown in the question. It produced the output:

GF:001<TAB>XXR
GF:00012<TAB>XXR
GF:01223<TAB>XXR
GF:001<TAB>XXXR3
GF:00012<TAB>XXXR3
GF:01223<TAB>XXXR3
GF:0666<TAB>XXXR3

(I took the liberty of deliberately misinterpreting <TAB> to be a 5-character sequence instead of a single tab character; you can easily fix the answer to handle an actual tab character instead.)

Explanation of the sed script:

• Find lines with more than one occurrence of GF:nnn separated by commas (we do not need to process lines that contain a single such occurrence). Do the rest of the script only on such lines. Anything else is passed through (printed) unchanged.
• Create a label so we can branch back to it
• Split the line into 3 remembered parts. The first part is the initial GF information; the second part is any other GF information; the third part is the field after the <TAB>. Replace this with the first field, <TAB>, third field, implausible marker pattern (@@@@@), second field, <TAB>, third field.
• Copy the modified line to the hold space.
• Delete the marker pattern to the end.
• Print.
• Swap the hold space into the pattern space.
• Remove everything up to and including the marker pattern.
• If we’ve done any work, go back to the redo label.
• Delete what’s left (it was printed already).
• End of script block.

This is a simple loop that reduces the number of the patterns by one on each iteration.