Shell Programming and Scripting

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

Code:

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

my file 2 would look like

Code:

AGTGCGTGCGTGCAATGTGCATGCGTGCAGTCGGGGGTAAGCTT........

Code:

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.

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

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

Code:

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

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