Hi, Here is my code written to identify the particular position which is after a string (chr*).
my input file looks some thing like this 
aanbb:anhn:iuopl:12345 chr1 12345 asnmkol * # kjiiii.....anmkij:lpolk:
+lopll:abnnj chr5 123222 polko * dddfgg ....

aaanbb:anhn:iuopl:aanjuj chr2 44345 asnmkol * # kjiiii.....anmkij:lpol
+k:lopll:abnnj chr7 567222 polko * dddfgg .

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i wanted to get the @pos as the immediate occurance after chr* as there are 2 such occurances in each line the first occrance has to be stored in pos[0] and second in pos1 for pos[0] pattern search has to be made wih in pos[0]+6 characters and same vs for pos1 but backwards
use strict;
use warnings;
open (my $fhConditions, "<1.txt"); 
my $l=6;
open (my $read, "<2.txt");
my @e = <$read>;
my $d = join('', @e );
$d =~ s/\s+//g;
while (my $line = <$fhConditions>) {
chomp $line;
my @pos = $line[$i] =~/chr*\s+(.+?)\s/g;
if($pos[0] =/[0-9]/)
{
my $match = substr($d,$pos[0],$l)
print "$line" if $match =~m/AAGCTT/;
}
if($pos[1] =/[0-9]/)
{
my $a = $pos[0]-$l;
my $match = substr($d,$a,$l);
print "$line" if $match =~m/AAGCTT/;
}
}

[download]
ERRORS
Global symbol "@line" requires explicit package name at restriction.pl
+ line 11.
Global symbol "$i" requires explicit package name at restriction.pl li
+ne 11.
syntax error at restriction.pl line 15, near ")
print"
Global symbol "$match" requires explicit package name at restriction.p
+l line 15.

[download]

In reply to How to get rid of the errors in my perl script by Anonymous Monk

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