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.

So perhaps you would be better off experimenting with the Bio::SeqIO module?

Hope that helps,

Athanasius <°(((>< contra mundum Iustus alius egestas vitae, eros Piratica,

In reply to Re: How can I get the values of codon usage using the Bio::CUA module? by Athanasius
in thread How can I get the values of codon usage using the Bio::CUA module? by supriyoch_2008

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