I have the majority of my code running properly, but I am getting repeats of the header for each corresponding output instead of one iteration of the header for all corresponding output. I don't think I am explaining that well, so I have included my current output with the desired output. My code

#!/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]

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 One header for multiple results by lairel

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.