Hi modified the program but it is still giving some errors :(
#!/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 positi
+on 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 positio
+n %d\n",
$key, $positions{$key} );
next;
}
$index += 3 while ( ($index + 3) < $positions{$key} );
print "$key $positions{$key} " . substr($sequences{$key}, $index,
+3) . "\n";
}
}
}