How can I get the values of codon usage using the Bio::CUA module?

supriyoch_2008 has asked for the wisdom of the Perl Monks concerning the following question:

Hi PerlMonks,

I am interested in estimating a few parameters of codon usage from a coding sequence using the perl module "use Bio::CUA" retrieved from cpan. I have written a script s1.pl but it fails to work. The above module contains several other modules inside it. I am at my wit's end to solve the issue. I need help from perlmonks so that I can get the values of codon usage.

Here goes my script s1.pl:

 # Code begins here 
################################
# To estimate tAI,CAI & encp of cds:
################################
#!/usr/bin/perl
use warnings;
use strict;  

use Bio::CUA; # perl module

my $cds="ATGCGTCTCTTCAAAACGCGCAAATCCACGGATACCTACAGCACACTAGCCGCGCAGCAA
CAGCAACAGCAGCAGCAGCAACAACAACATCAAGCGGAAGGCAGCAACATTTCCCACAGC
AGCAACAGCAGCAGCAACAAGAGTCACACACCGGCAACATGCAGCAACAGACTGAACAAG
AGCATTGTGAGCAGCACCAGCATATCGTCATCGCTGCCTGATCTGCATGACAAGTCGCCC
GTCATGATCCTCAGCTGCACCACCCTGGCCAGCAATGGAGCCACCGCCACGGCAGCGGTC
ACAGCAACAGCCACCGGCACAGCAGCAACATCTGGCGGCTCGCTGCAGCAGCAACAACAG
CAGCATCTGCAACACCAGCAGCAGCAGCAGCCGTTACGCACGGCCACGCCCACGTGTCTG
CTGAGTGGCCGTCAGACGCCATCGGCCATATCGGTGATGTCGCTCCAAGAGGCCACCAGT
CTGCACCGCCAGCAACAGCAGCCACACCAGCCACCCACCATCTACGTGCCGGTGCCTACG
AAACTTGGCAACAATGTCAACACTGGCAACAGCTCGGCCACTCTGCTGCTCAGCTATGGC
AGCACCAGCAGCATCGCCAACCTGCAACAGCAGCAGCAGCAGCATGCCGCCCAGTACCAG
CAGTATGTTGCACAGCGGCTGCACGCCGCTTCCAGCAGTTGTTTGTACGAGAAGGGGTCG
AATGCCAGCGGTGGGGCGAGCAGCAACAAAAGCAGTCTATCCCTGACCCCAAATGGTCAC
TTGCCCGACTACAAGTTGGTGACAGCGATGCCAGTTGTTGTCCTGGACGATGAACACAAA
TCCAATTCATTGCCGGCCACTGAAGCGAGTCGCAACAGCAACAGCAGCAGCAACATGAAC
GGCAGCAGCAACAGCAACAGCCTTGACGTCAGCAACAGCAACTCGCATTCGGGGAGCTCC
ACTTCTTTGGCCAGCACCACGAGAAATGTTTTCACCTGGGGCAAGCGCATGAGTCGCAAA
CTGGATTTGCTGAAGCGGAGTGACTCGCCCGCCGCCGCCCACAAATCGCATTCGGATTTG
AGGAGTCTGTTCCACTCGCCAACGCACCACAAGAGTGGATCCGGTGGATCCAGCGGACCC
AGTTCGGCGAAGGCATCGGCCTCACCCACTGGCGGCCATCAGAACAGCTCCGGCTCCACG
ACCAGCACCCTCAAGAAGTGCAAGTCGGGGCCCATCGAGACCATCAAGCAGCGACACCAG
CAGCAGCAGCAGCAGCAGCAATCGGTTCAGGATGTGGGCACGGGACAGAGCCAGAGTGCT
CAGTCCACGCCCACGCATCAGTTCCAGGCGGCCGCCCGCCCACAGAAAGCGCTAAAGAAC
TTCTTCCATAGGATCGGGTCCACCGGCATGCTGAACCATCGCTCCCACAATCTCCTTAAG
GCTTCGGAGGCGGCTCAACAGGCCACCCCGGCAGCCACCACATTGTATAGGAGCAGCTCC
ACTAGCCAGCTGTCCAGCAGCTCCTATGTGAAGTGCGACGATCCCACCGAGGGACTGAAT
CTTCAGAGGGAGCAGCGGGAACAGCGTCTTCCGCGGATCGCCAGCCTGAAGTCCAGTAGC
TGCGATGACATAGCCAAGGTGAGCAGTTGCCTGACGGCCAGCACAAGTAGTGGCAGTGCC
GCAGGCAGCTTGGGCTCTCCTCCAAGTAGTGCAGCAGCTGGTGGAGGCGGAACTGCAAAC
AGCGGCCAACACGATCCCTCGCGTCGTGGTGCATTTCCTTACGCCTTCCTGCGATCACGT
CTCTCCGTTTTGCCAGAGGAGAACCACGGAAATGTACCAGGACACCTGAAGCAACAAATA
CAGCGGCAACGGGAGCAGCACCAGCAGCATCAGAGGGATCTCCTCCAGCAGGAGCAGACA
TCGTCGCCCCTTCCCCAGCGCCGATCCCCCGAACAGGCGATGCTGAACAATGTGTCACGC
AACGACAGCATCACCTCCAAGGACTGGGAACCACTTTACCAAAGATTAAGTAGTTGTCTA
AGTTCAAACGAGTCCGGCTACGACAGCGATGGGGGTGCGACGGGAGCCCGACTGGGCAAT
AATCTGAGCATCTCCGGCGGAGATACCGAATCTATTGCCTCGGGCACACTCAAGCGTAAC
TCGCTCATCTCCCTCAGCTCCTCGGAGGGCGTTGGAATGGGCATGGGCATGAGTCTGGGA
CTGGGTGCCCCATCGACGAGGAACAGCAGCATCTGCAGTGCTCCCGTGTCGCTGGGTGGC
TATAACTACGACTATGAGACGGAGACGATACGGCGACGATTCAGGCAGGTTAAGCTGGAG
CGCAAGTGCCAAGAGGACTACATCGGAATTGTCCTGTCGCCCAAAACGGTGATGACCAAT
AGCAATGAGCAGCAGTACAGGTATCTCATCGTGGAACTGGAACCCTATGGCATGGCCCAA
AAGGATGGTCGCCTTCGCCTGGGTGACGAGATCGTCAACGTAAATGGAAAACACCTGCGA
GGCATTCAATCCTTTGCAGAGGTTCAGCGCCTGTTGAGCAGCTTTGTGGACAACTGTATC
GACCTGGTGATTGCTCACGATGAGGTGACGACGGTAACTGATTTCTACACCAAAATCCGT
ATCGATGGGATGAGCACGCAGCGCCATCGGCTGAGTTATGTGCAACGCACACAGAGCACA
GACAGTCTGAGCAGCATGCAGAGTCTGCAGCTGCAGCAGGAGAGGATTCAGGGTCACAAT
ACGGAACAGGAGCAGGAGGCCCAGGGCGAGGATCAGTGCGATGCGCGTTCAATGGCCAGC
GTCAGCACAATGCCCACTCCGATGCCGCTGATGCAGCATCGTCGGAGCTCCACGCCCAGG
CACTCACTGGACGTCGGTGCGCCGGAGCATGAGCTCCTCAGGAGGCGGGCGCGCAGCTCC
TCAGGTCAGCGCAGCTTGGCTCTAACACCGACCCCACTCTTTGCCAGCGGCAGCAGCAGT
TGCTCCTCCTCCCCTAACCACCGGTTGCTGGATAACGAGAACGACCCTGCTAACGACACC
GATTCCTATACGCCAGTGTATGCAAATCGGGCGGCAAGCGTGTGCGTGGCCTCCTCCCTG
GCGGACGATGAGAAGTGGCAGTTACTGGCCCGAAAGCGCTGCTCGGAGGGTTCCGCCCTA
TCCGCTACACCGAACCCGCAGCAATTTGGCCAGCGCACTCACTACGCCAGAAACTCCATC
AATCTGGCCAACTCGCATTACCGCTCGCTCCGATTTGCCCACTCGCGGCTGAGTTCGTCT
CGCCTTAGTCTGTTCATGCAGGCACCGCCTAACAGTCTAACCGTCGGAGAAGGAGTCGCT
AACACCCCATCCTCTACAGCTACCACAACCACTGATCTCACTAACCAGCAGCAACAGCAG
CAAAACCAGCAACAGACACACCAATCACTGTACATCAAGCACTCGCCAAAGAGCGTCTCA
TTGTTCTCGCCTAATCCCTATGTTAACGCCTCATCCTCACCAGCTTCGGCATCCACATCA
GCGGGTGCCGGCTCCTCCCTGGCACCGCCAGCCGCTGCCCTAATGCATCACAGGCCATCG
CTTCCGGTGGCCAAGCTAACAATACGCGACGAGGAAATGGCGGAGGTCATCCGTGCGTCG
ATGAGCGAGGGTAGTGGACGTTGCACCCCGAAGACTATAACCTTCTTTAAGGGACCTGGA
CTGAAATCGTTGGGCTTCAGCATAGTGGGAGGTCGAGATTCGCCAAAGGGCAACATGGGA
ATTTTTGTAAAGACCGTGTTTCCCTCAGGCCAGGCAGCCGATGATGGCACACTGCAAGCG
GGCGACGAGATTGTAGAGATCAATGGAAACTCTGTGCAGGGCATGAGTCATGCCGAAACC
ATAGGACTCTTTAAGAACGTAAGAGAGGGCACCATTGTGCTAAAAATCTTAAGAAGAAAA
TTACAGAAAGCTAAATCGATGGGTTGCTAG"; 

$cds=~ s/\s//g; 

##########################################################
# The following code has been taken from example of module:
########################################################## 

my $calc = Bio::CUA::CUB::Calculator->new(
       -codon_table => 1,
           -tAI_values  => 'tai.out' # from Bio::CUA::CUB::Builder
               );

# create an IO to a sequence file 
    my $io = Bio::CUA::SeqIO->new($cds); 

# read each sequence as a Bio::CUA::Seq object from this io

    while (my $seq = $io->next_seq)

       {
       my $tai = $self->tai($seq); 
       my $CAI = $self->cai($seq);
       my $encp =$self->encp_r($seq,[$minTotal,[$A,$T,$C,$G]]);


        printf("%10s: %.7f\n", $seq->id, $tai);
        printf("%10s: %.7f\n", $seq->id, $CAI);
        printf("%10s: %.7f\n", $seq->id, $encp);

     my $tai_val=printf("%10s: %.7f\n", $seq->id, $tai);
     my $CAI_val=printf("%10s: %.7f\n", $seq->id, $CAI);
     my $encp_val=printf("%10s: %.7f\n", $seq->id, $encp);

print "\n Results of Cds:
 tAI value=$tai_val; CAI value=$CAI_val; encp value=$encp_val\n"; 

        }  
exit;
[download]

I get the following results in cmd:

 Microsoft Windows [Version 6.1.7600]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.

C:\Users\x>cd desktop

C:\Users\x\Desktop>s1.pl
Global symbol "$self" requires explicit package name at C:\Users\x\Des
+kto
p\s1.pl line 97.
Global symbol "$self" requires explicit package name at C:\Users\x\Des
+kto
p\s1.pl line 98.
Global symbol "$self" requires explicit package name at C:\Users\x\Des
+kto
p\s1.pl line 99.
Global symbol "$minTotal" requires explicit package name at C:\Users\x
+\De
sktop\s1.pl line 99.
Global symbol "$A" requires explicit package name at C:\Users\x\Deskto
+p\s
1.pl line 99.
Global symbol "$T" requires explicit package name at C:\Users\x\Deskto
+p\s
1.pl line 99.
Global symbol "$C" requires explicit package name at C:\Users\x\Deskto
+p\s
1.pl line 99.
Global symbol "$G" requires explicit package name at C:\Users\x\Deskto
+p\s
1.pl line 99.
Execution of C:\Users\x\Desktop\s1.pl aborted due to compilation error
+s.

C:\Users\x\Desktop>
[download]

Comment on How can I get the values of codon usage using the Bio::CUA module? Select or Download Code

Replies are listed 'Best First'.

Re: How can I get the values of codon usage using the Bio::CUA module?
by Athanasius (Archbishop) on Nov 09, 2015 at 04:12 UTC

Hello supriyoch_2008,

The changes proposed by u65 are a good start, but in addition I’ve had to (1) change:

use Bio::CUA; # perl module
[download]

to:

use Bio::CUA::CUB::Calculator;
use Bio::CUA::SeqIO;
[download]

(2) create an empty file tai.out; (3) put the coding sequence in a file cds.dat and change:

my $io = Bio::CUA::SeqIO->new($cds);
[download]

to:

my $io = Bio::CUA::SeqIO->new(-file => 'cds.dat');
[download]

(4) change three occurrences of printf to sprintf:

my $tai_val  = sprintf "%10s: %.7f\n", $seq->id, $tai;
my $CAI_val  = sprintf "%10s: %.7f\n", $seq->id, $CAI;
my $encp_val = sprintf "%10s: %.7f\n", $seq->id, $encp;
[download]

But I’m still not getting meaningful output. :-( You need to specify for the PerlMonks exactly what output you expect to get. Also, you will need to address the following warnings:

------------- WARNING Bio::CUA::CUB::Calculator -------------
MSG: CAI values for codons were not provided for this analyzer, so can
+ not calculate CAI for sequences

-------------------------------------------------------------

...

------------- WARNING Bio::CUA::CUB::Calculator -------------
MSG: No default base composition for seq  '', so no GC-corrected ENC

-------------------------------------------------------------
[download]

But I note that the documentation for Bio::CUA::SeqIO says that it is:

a package to parse sequence file if module Bio::SeqIO is unavailable in the system.