Deleting extension only from the first column

Question

I have a file like this with tab separated two columns:

 ENSG00000242268.2    0.07563
 ENSG00000270112.3    0.09976
 ENSG00000167578.15   4.38608
 ENSG00000273842.1    0.0
 ENSG00000078237.5    4.08856

I would like to remove the numeric extensions from the end in the 1st column, so the output will be:

 ENSG00000242268    0.07563
 ENSG00000270112    0.09976
 ENSG00000167578    4.38608
 ENSG00000273842    0.0
 ENSG00000078237    4.08856

Simply doing sed 's/\..*$//' returns only first column value and using awk with field separator '.' , awk -F'.' removes the values from second column too as there are decimal numbers.

A similar question has been answered here: removing extensions in a column

I am still not being able to delete just from column 1st only.

Answer 1

awk solution:

awk -F'\t' '{sub(/\..+$/,"",$1)}1' OFS='\t' file

• -F'\t' - field separator

• sub(/\..+$/,"",$1) - removes . with following chars from the 1st field at once

The output:

ENSG00000242268 0.07563
ENSG00000270112 0.09976
ENSG00000167578 4.38608
ENSG00000273842 0.0
ENSG00000078237 4.08856

---

Or with simple sed approach:

sed 's/\.[0-9]*//' file

Answer 2

just do:

sed 's/\(.[0-9]\+\) / /' 

it will only match the first decimal part and delete it.

on your sample:

echo "ENSG00000242268.2    0.07563
>  ENSG00000270112.3    0.09976
>  ENSG00000167578.15   4.38608
>  ENSG00000273842.1    0.0
>  ENSG00000078237.5    4.08856" | sed 's/\(.[0-9]\+\) / /'
ENSG00000242268    0.07563
ENSG00000270112    0.09976
ENSG00000167578   4.38608

edit if you have tabs then try this:

sed 's/\(.[0-9]\+\)\( \|\t\)\2/' 

Answer 3

We may match a versioned Ensembl human gene "stable" ID with the extended regular expression ENSG[0-9]{11}\.[0-9]+.

Using this with sed:

$ sed -r 's/(ENSG[0-9]{11})\.[0-9]+/\1/' file.in >file.out

This does not rely on the delimiter between columns or where on the line the identifier occurs.

Answer 4

$ awk -F'[\t.]' -v OFS='\t' '{print $1,$3 "." $4}'
ENSG00000242268 0.07563
ENSG00000270112 0.09976
ENSG00000167578 4.38608
ENSG00000273842 0.0
ENSG00000078237 4.08856

Answer 5

With Bash using substring removal:

#!/usr/bin/env bash

file='file.txt'

while read -r i; do

  a=$( <<< "${i}" cut -d $'\t' -f 1 )
  a=${a%.*}
  b=$( <<< "${i}" cut -d $'\t' -f 2- )

  printf '%s\t%s\n' "${a}" "${b}"

done < "${file}"

Answer 6

Perl solution:

perl -pe 's/\.\d+//

• \.\d+ matches the first '.' followed by 1 or more digit.
• s/pattern// will delete the selected pattern.