#!/usr/bin/perl
use strict;
use warnings;
use diagnostics;

unless (open (INFILE, "<", "/scratch/SampleDataFiles/test.fasta")){
        die "Unable to open file", $!;
}

local $/ = ">";
#find and print desired sequence

while (<INFILE>) {

        chomp; #always chomp

                if ( $_ =~ /^(.*?)$(.*)$/ms ) { #match first line as header

                        my $header = $1; #assign the parts of the match

                                my $seq = $2;

                        $seq =~ s/\n//g; #get rid of whitespace


                                while($seq =~ /([VILMFWCA]{8,})/g){ #search for desired sequence

                                        my $location = pos($seq); #find location

                                                my $length = length($1); #determine length

                                                print "Hydrophobic stretch found in: ", $header, "\n"; #printing outputs for results

                                                print $1, "\n";
                                        print "The match was at position: ", $location - $length + 1, "\n\n";

                                }



                }
}
close INFILE;