getting no output with my perl program

Shell Programming and Scripting
1

hi,
i have posted the same kind of the question in some other forum of the same site. but realized that it is supposed to be here so i am reposting it .this is the perl script written to check for particular pattern.

my file 1 would look like this

hwk:678:9878:asd:09: abc cfgb 12 nmjk ......
hwk:879:0998:njmd:09: hyc chhgb 16 nmjk ......

my file 2 would look like

AGTGCGTGCGTGCAATGTGCATGCGTGCAGTCGGGGGTAAGCTT........

open(fhconditions, "<1.txt");
$l=250;
open(READ,"<2.txt");
@e=<READ>;
$a=join(" ",@e);
$a=~s/\s+//gi;
while (my $line = <$fhConditions>) {
chomp $line;
my @info = split("\t" , $line);
for($i=0;$i<length($a);$i++)
{
my $match = substr($a,$info[3],$l);
print "info[3]";
if ($match =~m/AAGCTT/)
{
print "$line\n";	
}
}
}
print "position:"

I want to get the positions from file 1 eg:12 and search from that position to 250 characters ahead in second file for the desired pattern. once it found i want to know where among 250 characters it was found. hope i am clear. i am just a beginer and my code may contain many mistakes.

2

Reason you are getting no output is you used different case for fhconditions in open and while lines.

3

Also, stick to one style of using file handles. Lose the dollar symbol in while loop.

open fhconditions, "< 1.txt";
.
.
while (my $line = <fhconditions>) {
4

thank you very much for your suggestions but how to get the position of match?