CODEWITHSUNDEEP
linuxshellunixawk
Marjer
Marjer

Reputation: 1403

Compare two files of different columns and print different columns

I want to compare 2nd column of file2 with 1st column of file1. If they are equal i want to add the 2nd column of file1 to file2 as shown in output.txt.

file2

chr5    ENST00000514151    utr5    0    +
chr5    ENST00000512281    utr5    0    +
chr5    ENST00000512281    utr5    0    +
chr5    ENST00000512281    utr5    0    +

file1

ENST00000512281    a
ENST00000504031    b
ENST00000776348    c

output.txt

chr5    a    ENST00000512281    utr5    0    +
chr5    a    ENST00000512281    utr5    0    +
chr5    a    ENST00000512281    utr5    0    +

I was able compare the files with 

awk 'NR==FNR{a[$1];next}$2 in a{print}' file1 file2

This gives below output:

chr5    ENST00000512281    utr5    0    +
chr5    ENST00000512281    utr5    0    +
chr5    ENST00000512281    utr5    0    +

But I do not know how to add the 2nd colum of file1 into the output.

Upvotes: 1

Views: 5870

Answers (1)

Håkon Hægland
Håkon Hægland

Reputation: 40778

You can store the value of $2 in file1 into the array using a[$1]=$2. So you could try:

awk '
   NR==FNR{ 
     a[$1]=$2 ; next }
   $2 in a {
     $1=$1 FS a[$2]
     print 
   }' file1 file2

Output:

chr5 b ENST00000504031 utr5 0 +
chr5 b ENST00000504031 utr5 0 +
chr5 a ENST00000512281 utr5 0 +
chr5 a ENST00000512281 utr5 0 +
chr5 a ENST00000512281 utr5 0 +

Explanation:

  • This modifies $1 in file2 using $1=$1 FS a[$2] where FS is the default field separator, which is a space.. and then rebuilds the record, such that it can be printed by print later..
  • The print can be simplified to a 1 if desired.. Like $2 in a { $1=$1 FS a[$2] }1
  • Note that this rebuilds the record in file2 and thus any sequences of spaces or tabs will be truncated to a single space in the output. To keep the original formatting in file2 one could use the split() function in Gnu Awk version 4..

Upvotes: 2

Related Questions