parsing table using linux commands

upendra_35 · 11-28-2012, 10:16 PM

Hi i have a two column table as below

Code:

Bra033296	GO:0006355
Bra033296	GO:0003677
Bra033296	GO:0005634
Bra033295	GO:0005739
Bra033294	GO:0005634
Bra033294	GO:0006355
Bra033294	GO:0003677

Now i want to parse them as below

Code:

Bra033296       GO:0006355, GO:0003677, GO:0005634
Bra033295	   GO:0005739
Bra033294       GO:0005634, GO:0006355, GO:0003677

Is it possible with linux commands?

Thanks

pan64 · 11-29-2012, 12:42 AM

yes, sure, it is possible, you need to select the tools you want to use: awk/perl/sed.... What do you prefer?

upendra_35 · 11-29-2012, 02:33 AM

Quote:

Originally Posted by pan64

yes, sure, it is possible, you need to select the tools you want to use: awk/perl/sed.... What do you prefer?

Thanks....I don't have any preference.

colucix · 11-29-2012, 03:55 AM

What about awk?

Code:

awk '{ _[$1] ? _[$1] = _[$1] ", " $2 : _[$1] = $2 } END{ for ( i in _ ) printf "%s\t%s\n", i, _[i] }' file

upendra_35 · 11-29-2012, 12:45 PM

Quote:

Originally Posted by colucix

What about awk?

Code:

awk '{ _[$1] ? _[$1] = _[$1] ", " $2 : _[$1] = $2 } END{ for ( i in _ ) printf "%s\t%s\n", i, _[i] }' file

This is exactly what i need. I just made a small edit to remove the space after ",".

Code:

awk '{ _[$1] ? _[$1] = _[$1] "," $2 : _[$1] = $2 } END{ for ( i in _ ) printf "%s\t%s\n", i, _[i] }'

Anyway thanks for your help. Much appreciated.

David the H. · 11-30-2012, 10:09 AM

Please don't use php code tags. There's a bug that keeps them from properly adjusting to the display width. Besides, this isn't php. Just use regular code tags.

Thanks.

colucix · 11-30-2012, 10:52 AM

Quote:

Originally Posted by David the H.

Please don't use php code tags. There's a bug that keeps them from properly adjusting to the display width. Besides, this isn't php. Just use regular code tags.

Thanks.

Indeed. Changed to [CODE][/CODE].