#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

my $qfn1 = "File1.txt";
my $qfn2 = "File2.txt";

my %positions;
{
   open(my $fh, '<', $qfn1)
      or die("Cannot open file \"$qfn1\": $!\n");

 while ( <$fh> ) {
	chomp;
	my ( $key, $pos ) = split /\s+/;

	
	push @{ $positions{$key} }, $pos;
}
}
print Data::Dumper->Dumpxs( [ \ %positions ], [ qw{ *positions } ] );
my %sequences;
{
   open(my $fh, '<', $qfn2)
      or die("Cannot open file \"$qfn2\": $!\n");

   my $key;
   while (<$fh>) {
       if ( s/^>// ) {
           $key = ( split /\|/ )[1];
       }
       else {
           chomp;
           $sequences{$key} .= $_;
       }
   }
}
for my $key (sort keys %positions)
            {
               for my $key (keys %{$positions{$key}})
               {
   foreach my $value (@) {
    if (! exists( $sequences{$key} )) {
        warn "KEY $key in File1 not found in File2\n";
        next;
    }
    if ( length( $sequences{$key} ) < $positions{$key} ) {
        warn "KEY $key: File2 string length too short for File1 position value\n";
        next;
    }
     my $index = rindex( $sequences{$key}, "ATG", $positions{$key} );
    if ( $index < 0 ) {
        warn sprintf( "KEY %s: No ATG in File2 string prior to position %d\n",
                      $key, $positions{$key} );
        next;
    }
    $index += 3 while ( ($index + 3) < $positions{$key} );
    print "$key $positions{$key} " . substr($sequences{$key}, $index, 3) . "\n";
}
    }
}