Re: Iso electric point calculation using perl

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

Comment on Re: Iso electric point calculation using perl Select or Download Code

Replies are listed 'Best First'.
Re^2: Iso electric point calculation using perl by yuvraj_ghaly (Sexton) on Jul 22, 2013 at 05:28 UTC
I run this code of yours but nothing happened. Is ther any addition to this code?	[reply]
Re^2: Iso electric point calculation using perl by yuvraj_ghaly (Sexton) on Jul 22, 2013 at 05:00 UTC
thank you for the code but I have one thing to ask. I should incorporate this code into my perl script. m I right?	[reply]
Re^3: Iso electric point calculation using perl by erix (Prior) on Jul 22, 2013 at 05:19 UTC
No. I didn't look at your code. It's obviously too long and you said it didn't do what you wanted and I was only interested in the code on the rutgers.edu website so I made a program to wrap that into. Just take the code I gave you, save it as a file, and copy the code from the rutgers.edu website into the `calculate_protein_details` sub that I gave you (except the first line (of the rutgers.edu code)). Then it just works. I tried it again, just now. If you want it to read the sequence from a fasta file, add that functionality afterwards, but that's a completely different 'problem'. Remember: when things don't work you have to simplify till you understand why it doesn't.	[reply] [d/l]


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