Re: How to get rid of the errors in my perl script

[davido]

in reply to How to get rid of the errors in my perl script

$line is a scalar variable that you declare in line 9. $line[$i] is an element of an array named @line, which is a totally different (undeclared) variable that has no relationship to the scalar named $line.

The scalar variable $i makes its first appearance in your script in line 11. What value is it supposed to contain? If you don't declare it, and don't assign it a value, it's probably not going to do what you need it to do.

You're missing a semicolon after the substr(...) call on line 14. (It's usually a good idea to look at the line right above where syntax errors are reported.)

Finally: Install perltidy and pass your script through it. Judicious use of white-space makes code more readable, and errors easier to detect.

These only address the superficial issues: the error messages you're seeing. Once you fix those issues, it becomes time to debug the logic.

[Anonymous Monk]

open (my $fhConditions, "<a.txt"); 
my $l=6;
open (my $read, "<b.txt");
my @e = <$read>;
my $d = join('', @e );
$d =~ s/\s+//g;
while (<$fhConditions>) {
    push (my @line, $_);
$count++;
}
for ($i = 0; $i < $count; $i++)
{
my @pos = my $line[$i] =~ /chr*\s+(.+?)\s/g;
if($pos[0] =~/[0-9]/)
{
my $match = substr($d,$pos[0],$l);
print "$line[$i]" if $match =~m/AAGCTT/;
}
if($pos[1] =~/[0-9]/)
{
my $a = $pos[0]-$l;
my $match = substr($d,$a,$l);
print "$line[$i]" if $match =~m/AAGCTT/;
}
}

this the code modified after the suggestions. but still i am getting some error

yntax error at restriction.pl line 13, near "$line["
Execution of restriction.pl aborted due to compilation errors.

[ig]

You should remove my from line 13. It doesn't belong there and is causing this error.