#!/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;

##</code><code>##

Hydrophobic stretch found in: P30450 | Homo sapiens (Human). | NCBI_TaxID=9606; | 365 | Name=HLA-A; Synonyms=HLAA;

 

AVVAAVMW

The match was at position: 325

 

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_TaxID=9606; | 1401 | Name=DISP2; Synonyms=DISPB, KIAA1742;

 

VAVLMLCLAVIFLC

The match was at position: 170

 

LLALVAIFF

The match was at position: 493

 

IWICWFAALAA

The match was at position: 705

 

LALALAFA

The match was at position: 970

##</code><code>##

Hydrophobic stretch found in: P30450 | Homo sapiens (Human). | NCBI_TaxID=9606; | 365 |    Name=HLA-A; Synonyms=HLAA;

AVVAAVMW

The match was at position: 325

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_TaxID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;

VAVLMLCLAVIFLC

The match was at position: 170

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_TaxID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;

LLALVAIFF

The match was at position: 493

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_TaxID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;

IWICWFAALAA

The match was at position: 705

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_TaxID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;

LALALAFA

The match was at position: 970