Question

The following is the script for finding consecutive substrings in strings.

use strict;
use warnings;

my $file="Sample.txt";
open(DAT, $file) || die("Could not open file!");

#worry about these later
#my $regexp1 = "motif1";
#my $regexp2 = "motif2";
#my $regexp3 = "motif3";
#my $regexp4 = "motif4";

my $sequence;

while (my $line = <DAT>) {
    if ($line=~ /(HDWFLSFKD)/g){
        {
        print "its found index location: ",
        pos($line), "-",  pos($line)+length($1), "\n";        
        }
        if ($line=~ /(HD)/g){
                print "motif found and its locations is: \n";
                pos($line), "-", pos($line)+length($1), "\n\n";
                }
                if ($line=~ /(K)/g){
                        print "motif found and its location is: \n";
                        pos($line), "-",pos($line)+length($1), "\n\n";
                        }
                        if ($line=~ /(DD)/g){
                                print "motif found and its location is: \n";
                                pos($line), "-", pos($line)+length($1), "\n\n";
                                }
}else {
        $sequence .= $line;
        print "came in else\n";
    }
}

It matches substring1 with string and prints out position where substring1 matched. The problem lies in finding the rest of the substrings. For substrings2 it starts again from the beginning of the string (instead of starting from the position where substring1 was found). The problem is that every time it calculates position it starts from the beginning of string instead of starting from the position of the previously found substring. Since substrings are consecutive substring1, substring2, substring3, substring4, their positions have to occur after the previous respectively.

Answer 1

I’m not a perl expert but you can use $- and $+ to track index location for last regex match found.
Below is code built on top of your code that explains this.

use strict;
use warnings;


my $file="sample.txt";
open(DAT, $file) || die("Could not open file!");

open (OUTPUTFILE, '>data.txt');

my $sequence;
my $someVar = 0;
my $sequenceNums = 1;

my $motif1 = "(HDWFLSFKD)";
my $motif2 = "(HD)";
my $motif3 = "(K)";
my $motif4 = "(DD)";

while (my $line = <DAT>) 
{
    $someVar = 0;
    print "\nSequence $sequenceNums: $line\n";
    print OUTPUTFILE "\nSequence $sequenceNums: $line\n";
        if ($line=~ /$motif1/g)
        {
                &printStuff($sequenceNums, "motif1", $motif1, "$-[0]-$+[0]");
                $someVar = 1;
        }


        if ($line=~ /$motif2/g and $someVar == 1)
        {
                &printStuff($sequenceNums, "motif2", $motif2, "$-[0]-$+[0]");
                $someVar = 2;
        }

        if ($line=~ /$motif3/g and $someVar == 2)
        {
                &printStuff($sequenceNums, "motif3", $motif4, "$-[0]-$+[0]");
                $someVar = 3;
        }

        if ($line=~ /$motif4/g and $someVar == 3)
        {
                &printStuff($sequenceNums, "motif4", $motif4, "$-[0]-$+[0]");
        }

        else 
        {
            $sequence .= $line;

            if ($someVar == 0)
            {
                &printWrongStuff($sequenceNums, "motif1", $motif1);
            }
            elsif ($someVar == 1)
            {
            &printWrongStuff($sequenceNums, "motif2", $motif2);
            }
            elsif ($someVar == 2)
            {
            &printWrongStuff($sequenceNums, "motif3", $motif3);
            }
            elsif ($someVar == 3)
            {
            &printWrongStuff($sequenceNums, "motif4", $motif4);
            }
        }
        $sequenceNums++;
}

sub printStuff
{
            print "Sequence: $_[0] $_[1]: $_[2] index location: $_[3] \n";
            print OUTPUTFILE "Sequence: $_[0]  $_[1]: $_[2] index location: $_[3]\n";
}

sub printWrongStuff
{
            print "Sequence: $_[0] $_[1]: $_[2] was not found\n";
            print OUTPUTFILE "Sequence: $_[0] $_[1]: $_[2] was not found\n";    

}

close (OUTPUTFILE);
close (DAT);

Sample input:

MLTSHQKKFHDWFLSFKDSNNYNHDSKQNHSIKDDIFNRFNHYIYNDLGIRTIA
MLTSHQKKFSNNYNSKQNHSIKDIFNRFNHYIYNDLGIRTIA
MLTSHQKKFSNNYNSKHDWFLSFKDQNHSIKDIFNRFNHYIYNDL