Modifying Text Column Wise with Sed/AWK

Question

I have an input data with three columns (tab separated) like this:

  a  mrna_185598_SGL 463
  b  mrna_9210_DLT   463
  c  mrna_9210_IND   463
  d  mrna_9210_INS   463
  e  mrna_9210_SGL   463

How can I use sed/awk to modify it into four columns data that looks like this:

a  mrna_185598 SGL   463
b  mrna_9210   DLT   463
c  mrna_9210   IND   463
d  mrna_9210   INS   463
e  mrna_9210   SGL   463

In principle I want to split the original "mrna" string into 2 parts.

Answer 1

gawk:

{
  print $1 "\t" gensub(/_/, "\t", 2, $2) "\t" $3
}

Answer 2

something like this

awk 'BEGIN{FS=OFS="\t"}{split($2,a,"_"); $2=a[1]"_"a[2]"\t"a[3] }1'  file

output

# ./shell.sh
a       mrna_185598     SGL     463
b       mrna_9210       DLT     463
c       mrna_9210       IND     463
d       mrna_9210       INS     463
e       mrna_9210       SGL     463

use nawk on Solaris

and if you have bash

while IFS=$'\t' read -r a b c
do
    front=${b%_*}
    back=${b##*_}
    printf "$a\t$front\t$back\t$c\n"
done <"file"

Answer 3

Provided they don't look too much different from what you've posted:

sed -E 's/mrna_([0-9]+)_/mrna_\1\t/'

Answer 4

you dont need to use sed. instead use tr

cat *FILENAME* | tr '_[:upper:]{3}\t' '\t[:lower:]{3}\t' >> *FILEOUT*

cat FILENAME will print out the files witch will then be piped ('|') to tr (translate). tr will replace anything that has an underscore followed by 3 uppercase characters and then a tab with a tab instead of the underscore. Then it will append it to FILEOUT.

Answer 5

$ cat test.txt
  a  mrna_185598_SGL 463
  b  mrna_9210_DLT   463
  c  mrna_9210_IND   463
  d  mrna_9210_INS   463
  e  mrna_9210_SGL   463

$ cat test.txt | sed -E 's/(\S+)_(\S+)\s+(\S+)$/\1\t\2\t\3/'
  a  mrna_185598    SGL 463
  b  mrna_9210  DLT 463
  c  mrna_9210  IND 463
  d  mrna_9210  INS 463
  e  mrna_9210  SGL 463