bash while loop failing while using sed

Your script is very inefficient. Using the while-loop you read each line of file1. This is N operations. Per line you process with the while loop, you reproscess the full file1, making it an N*N process. However, in the sed, you grep file2 constantly. If file2 has M lines, this becomes an N*N*M process. This is very inefficient.

On top of that there are some issues:

• You updated file1 inplace because you use the -i flag. An inplace update does not provide any output, so file3 will be empty.
• You are reading file1 with the while-loop and at the same time you update file1 with sed. I don't know how this will react, but I don't believe it is healthy.
• If $b is not in file2 you would, according to your logic, have a line with only a single column. This is not what you expect.

A fix of your script, would be this:

while read -r a b; do
  c=$(grep "$b" file2)
  [[ "$c" == "" ]] || echo "$a $c"
done < file1 > file3

which is still not efficient, but it is already M*N. The best way is using awk

note: as a novice, always parse your script with http://www.shellcheck.net
note: as a professional, always parse your script with http://www.shellcheck.net

Could you please try following.

awk 'FNR==NR{a[$2]=$1;next} {for(i in a){if(match($0,"^"i)){print a[i],$0;continue}}}'  file1  file2

Adding a non-one liner form of solution:

awk '
FNR==NR{
  a[$2]=$1
  next
}
{
  for(i in a){
    if(match($0,"^"i)){
      print a[i],$0
      continue
    }
  }
}
'  Input_file1  Input_file2

Explanation: Adding detailed explanation for above code.

awk '                             ##Starting awk code from here.
FNR==NR{                          ##Checking condition if FNR==NR then do following.
  a[$2]=$1                        ##Creating array a whose index is $2 and value is $1.
  next                            ##next will skip all further statements from here.
}
{                                 ##Statements from here will run for 2nd Input_file only.
  for(i in a){                    ##Traversing through array a all elements here.
    if(match($0,"^"i)){           ##Checking condition if current line matches index of current item from array a then do following.
      print a[i],$0               ##Printing array a whose index is i and current line here.
      continue                    ##Again take cursor to for loop.
    }
  }
}
'  Input_file1  Input_file2       ##Mentioning all Input_file names here.