Ramya715 has asked for the wisdom of the Perl Monks concerning the following question:

I am a perl beginner and need some help with regex Input for this code is : aatgatgataaggtaaggtatgatgatgatgatgatagtagannnnnnnnnatgcatga'/atgca.atgactagca/atgactagcaaggtaaggtaaggtaaggtaaggtatgatgatgannnn./atgatgactagactgacaaggtaaggtaaggtatgatgatgatcgatgacgat... and so on

Here i am trying to assign input file as a scalar variable and trying to find a match of "aaggtaaggt" and then skip some 100 characters whether they are alphabets or symbols or any wildcard characters after skipping exact 100 characters, i am again asking code to start search for match again and every time it finds a match , i am counting and asking to print..

As of my knowledge i have tried using substr of match as pos1 and had set offset for 100 and then assigned that as initial pos for reading second match , but failed to get the correct output, then tried here post match as $' but doubt whether it is correct or not.

#!/usr/bin/perl 
$count1 = 0; 
open (FILE, "INPUT") || die "cannot open $!\n"; 
while ($line = <FILE>){ 

if(($line=~m/(aaggt){2}/ig)&&($'=~m/([atgcn]{100,})/i)) { 
$count1 ++ ; 
print " " ,$1, "\t"; 
print "count1 \t " ,$count1 , "\n" ; 
} 

}

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Please, help me figuring out this task. Thanks

Replies are listed 'Best First'.
Re: Need Help with reg ex
by GrandFather (Saint) on Oct 28, 2009 at 04:07 UTC

    If I understand what you are trying to achieve then you can do it using a single regular expression match:

    use strict;
use warnings FATAL => 'all';

my $count1 = 0;

my $line = do {local $/; <DATA>;};

$line =~ s/\n//g;

while (($line =~ m/(?:aaggt){2}([atgcn]{100,})/ig)) {
    $count1++;
    print " $1\tcount1 \t $count1\n";
}

__DATA__
aatgatgataaggtaaggtatgatgatgatgatgatagtagannnnnnnnnatgcatgaatgcaatgact
+agcaatgac
tagcaaggtaaggtaaggtaaggtaaggtatgatgatgannnnatgatgactagactgacaaggtaaggt
+aaggtatga
tgatgatcgatgacgat

    [download]

    As an aside, note that you should always use strictures (use strict; use warnings;). You should also use the three parameter version of open and use lexical file handles:

    open my $inFile, '<', $fileName or die "cannot open $fileName: $!\n";

    [download]
    True laziness is hard work
[reply]
[d/l]
[select]
Re: Need Help with reg ex
by bichonfrise74 (Vicar) on Oct 28, 2009 at 04:07 UTC
    Based on how I understand your question, this is how I would do it. 
    #!/usr/bin/perl

use strict;

my $count = 0;
while (<DATA>) {
    while ( /(aaggt)/g ) {
        $count++;
        print "$1 - Count: $count\n";
        print "Found at position : " . pos(), "\n";
        pos() += 100;
    }
}

__DATA__
aatgatgataaggtaaggtatgatgatgatgatgatagtagannnnnnnnnatgcatga'/atgca.atg
+actagca/atgactagcaaggtaaggtaaggtaaggtaaggtatgatgatgannnn./atgatgactag
+actgacaaggtaaggtaaggtatgatgatgatcgatgacgat

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[d/l]

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