Hello, This question was posted and answered on StackOverflow: I have two files that I would like to match based on the first letter of the second column in File1 and the first letter of the third column in File2. For example:

File1 
1 H 35
1 C 22
2 H 20
2 C 30

File 2
A  1  HB2 MET 1
A  2  CA  MET 1
A  3  HA  ASP 2
A  4  CA  ASP 2

Output
1  MET  HB2 35
1  MET  CA  22
2  ASP  HA  20
2  ASP  CA  30

[download]
Below is my script: 
 #!/usr/bin/perl

use strict;
use warnings;

my %data;

open (SHIFTS,"file1.txt") or die;
open (PDB, "file2.txt") or die;

while (my $line = <PDB>) {
    chomp $line;
    my @fields = split(/\t/,$line);
    $data{$fields[4]} = $fields[2];
 }

 close PDB;

 while (my $line = <SHIFTS>) {
    chomp($line);
    my @columns = split(/\t/,$line);
    my $value = ($columns[1] =~ m/^.*?([A-Za-z])/ );
 }
 if (my $value = $data{"$_"})
    print "$columns[0]\t$fields[3]\t$value\t$data{$value}\n";

 close SHIFTS;
 exit;

[download]

I am not sure how to implement the match, my if statement above is not correct. Any advice would be greatly appreciated.

In reply to Match two files using regex by chemshifts

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