Text Processing – Merging Columns from Two Separate Files

$ awk 'FNR==NR{a[$1]=$2;next} ($1 in a) {print $1,a[$1],$2}' file2 file1
aa 45 32
bb 31 15
cc 50 78

Explanation:

awk implicitly loops through each file, one line at a time. Since we gave it file2 as the first argument, it is read first. file1 is read second.

• FNR==NR{a[$1]=$2;next}

  NR is the number of lines that awk has read so far and FNR is the number of lines that awk has read so far from the current file. Thus, if FNR==NR, we are still reading the first named file: file2. For every line in file2, we assign a[$1]=$2.

  Here, a is an associative array and a[$1]=$2 means saving file2's second column, denoted $2, as a value in array a using file2's first column, $1, as the key.

  next tells awk to skip the rest of the commands and start over with the next line.

• ($1 in a) {print $1,a[$1],$2}

  If we get here, that means that we are reading the second file: file1. If we saw the first field of the line in file2, as determined by the contents of array a, then we print out a line with the values of field 2 from both files.

You can do it using the sub function in awk:

awk 'sub(/./,"& ",$2)1;' file

If you want tab-separated output, you can use:

awk -v OFS="\t" 'sub(/./,"&\t",$2)1;' file

Or in a variety of other tools:

• Perl

  perl -alne '$F[1]=~s/./$& /; print "@F"' file
  

  Or, for tab-separated output:

  perl -alne '$F[1]=~s/./$&\t/; print join "\t",@F' file
  

• GNU sed

  sed -r 's/\S+\s+\S/& /' file
  

• Other sed

  sed  's/^[[:alnum:]]*[[:blank:]]*./& /' file
  

• Shell

  while read -r snp nt rest; do 
      printf "%s\t%s\t%s\t%s\n" "$snp" "${nt:0:1}" "${nt:0:1}" "$rest"
  done < file