CODEWITHSUNDEEP
linuxunixsedawktext-processing
neversaint
neversaint

Reputation: 64084

Modifying text column wise with sed/awk

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.

Upvotes: 0

Views: 2100

Answers (7)

Claes Wikner
Claes Wikner

Reputation: 1517

gawk '{$1=$1; $0=gensub(/_/,"\t",2);print}' file

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

Upvotes: 1

potong
potong

Reputation: 58578

This might work for you (GNU sed):

sed 's/_/\t/2' file

Replace the second occurrence of a _ by a tab.

Upvotes: 0

ghostdog74
ghostdog74

Reputation: 343201

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"

Upvotes: 2

Kyle Butt
Kyle Butt

Reputation: 9810

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

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

Upvotes: 1

Damodharan R
Damodharan R

Reputation: 1507

$ 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

Upvotes: 1

sgmitchell
sgmitchell

Reputation: 61

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.

Upvotes: 1

Ignacio Vazquez-Abrams
Ignacio Vazquez-Abrams

Reputation: 799580

gawk:

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

Upvotes: 2

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