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.

In reply to Re: How can I get the values of codon usage using the Bio::CUA module? by u65
in thread How can I get the values of codon usage using the Bio::CUA module? by supriyoch_2008

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.