Beefy Boxes and Bandwidth Generously Provided by pair Networks
Think about Loose Coupling
 
PerlMonks  

Re: Iso electric point calculation using perl

by erix (Vicar)
on Jul 19, 2013 at 23:09 UTC ( #1045408=note: print w/ replies, xml ) Need Help??


in reply to 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...) }

Output:

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

( 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
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?

      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.

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?

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://1045408]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others browsing the Monastery: (7)
As of 2015-07-04 22:30 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    The top three priorities of my open tasks are (in descending order of likelihood to be worked on) ...









    Results (60 votes), past polls