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

by u65 (Chaplain)
on Nov 09, 2015 at 02:08 UTC ( #1147234=note: print w/replies, xml ) Need Help??


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

I don't know what you've tried, but those errors are from the undeclared variables cited. If you have just copied the erroneous code, you must have missed the earlier part where they were declared.

Update: Try replacing all instances of $self with $calc. Then change this line:

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

to this:

my $encp =$calc->encp_r($seq);

All I did was remove the optional args from the encp_r method.

Update 2: I just saw this reference (http://biorxiv.org/content/early/2015/11/03/019265) on today's Perl Weekly which looks like something of interest to Perl Bio folks like supriyoch_2008.

Replies are listed 'Best First'.
Re^2: How can I get the values of codon usage using the Bio::CUA module?
by supriyoch_2008 (Monk) on Nov 12, 2015 at 15:10 UTC

    Hi u65,

    Thank you very much for your suggestions. The reference cited by you is really very good and will be of great use to me in my future endeavor.

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