I am very new to perl, and have been trying to get this code right, but I am completely lost. I have tried a few variations but have no idea where I am going wrong or what I need to do. I currently get no error messages of any sort. The program is supposed ot read a fasta file, searching for the sequence VILMFWCA, and the output is the header that contains that sequence and then the sequence and location. Here is what I have 

#!/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 h
+eader

                        my $header = $1; #assign the parts of the matc
+h

                                my $seq = $2;

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


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

                                        my $location = pos($seq); #fin
+d location

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

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

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

                                }



                }
}
close INFILE;

[download]

updates with where I am at now, but now I am getting too much output, every time it finds the stretch it prints the header instead of once per header, I tried moving the print command up but it didn't do it. The output is supposed to look like this: 

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

 

AVVAAVMW

The match was at position: 325

 

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_Ta
+xID=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

[download]

but my current output is like this: 

Hydrophobic stretch found in: P30450 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 365 |    Name=HLA-A; Synonyms=HLAA;
AVVAAVMW
The match was at position: 325

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;
VAVLMLCLAVIFLC
The match was at position: 170

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;
LLALVAIFF
The match was at position: 493

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;
IWICWFAALAA
The match was at position: 705

Hydrophobic stretch found in: A7MBM2 | Homo sapiens (Human). | NCBI_Ta
+xID=9606; | 1401 |    Name=DISP2; Synonyms=DISPB, KIAA1742;
LALALAFA
The match was at position: 970

[download]

I'm so close

In reply to Where am I going wrong? by lairel

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