Looking at the original code from that page, I conclude that it is the body of a subroutine, and not a standalone program.

So, wrap it in a subroutine (say, calculate_protein_details and call that subroutine with 2 arguments: a protein sequence $protein (the input), and an empty hash %results (the output, which whill be filled in by the subroutine). 

#!/usr/bin/perl
use strict;
use warnings;
main();
exit;
sub main {

  # I took this example sequence from uniprot.org
  # from entry >sp|P02754|LACB_BOVIN Beta-lactoglobulin

  my $protein = "MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDAQSA
+PLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKIDALNENKVLVLDTDYKKYLLFC
+MENSAEPEQSLACQCLVRTPEVDDEALEKFDKALKALPMHIRLSFNPTQLEEQCHI";
  my %results = ();

  calculate_protein_details( $protein, \%results);
  while (my ($k,$v) = each %results)
  {
    print $k, "  =>  ", $v, "\n";
  }
}
sub calculate_protein_details {

  my ($protein, $hash_ref) = @_;

  # copy here the code (except the first line) from
  # http://www-nmr.cabm.rutgers.edu/bioinformatics/ZebaView/help.html
  #     (not your mangled code...)
}

[download]

Output: 

extinction  =>  16960
pI  =>  4.93
MW_N15  =>  20105.52
MW  =>  19883.00
MW_SeMet  =>  20117.50
MW_N15_C13  =>  20986.05

[download]

( Don't complicate matters and solve one problem at a time. Reading a fasta file to get its sequence is a entirely separate thing )

UPDATED: restructured the code a bit

In reply to Re: Iso electric point calculation using perl by erix
in thread Iso electric point calculation using perl by yuvraj_ghaly

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