[Bioperl-l] POD rendering question/problem (was [Fwd: What is CPAN doing?])

[Robert Buels]

Hi search.cpan.org maintainers,

For one of the methods in BioPerl, a good portion of the POD that's in 
the source [1] isn't being rendered into HTML on its search.cpan.org 
page [2].

We'd like to get this POD displaying properly, either by us (BioPerl) 
tweaking the POD on our end, or by you guys tweaking whatever process is 
  making the HTML.

So: do we need to tweak our POD to get it displaying properly?  If so, 
what needs to change in that POD?

Rob

[1] The source and POD in question:
http://search.cpan.org/src/CJFIELDS/BioPerl-1.6.1/Bio/PrimarySeqI.pm

[2] The HTML in question:
http://search.cpan.org/~cjfields/BioPerl-1.6.1/examples/root/lib/Bio/PrimarySeqI.pm#translate





-------- Original Message --------
Subject: [Bioperl-l] What is CPAN doing?
Date: Fri, 21 May 2010 14:52:19 -0400
From: Brian Osborne <briano at bioteam.net>
To: BioPerl List <Bioperl-l at lists.open-bio.org>

bioperl-l,

Here's the POD for the translate() method:

=head2 translate

  Title   : translate
  Usage   : $protein_seq_obj = $dna_seq_obj->translate

            Or if you expect a complete coding sequence (CDS) translation,
            with inititator at the beginning and terminator at the end:

            $protein_seq_obj = $cds_seq_obj->translate(-complete => 1);

            Or if you want translate() to find the first initiation
            codon and return the corresponding protein:

            $protein_seq_obj = $cds_seq_obj->translate(-orf => 1);

  Function: Provides the translation of the DNA sequence using full
            IUPAC ambiguities in DNA/RNA and amino acid codes.

            The complete CDS translation is identical to EMBL/TREMBL
            database translation. Note that the trailing terminator
            character is removed before returning the translated protein
            object.

            Note: if you set $dna_seq_obj->verbose(1) you will get a
            warning if the first codon is not a valid initiator.

  Returns : A Bio::PrimarySeqI implementing object
  Args    : -terminator    - character for terminator        default is *
            -unknown       - character for unknown           default is X
            -frame         - frame                           default is 0
            -codontable_id - codon table id                  default is 1
            -complete      - complete CDS expected           default is 0
            -throw         - throw exception if not complete default is 0
            -orf           - find 1st ORF                    default is 0
            -start         - alternative initiation codon
            -codontable    - Bio::Tools::CodonTable object
		   -offset        - offset for fuzzy locations      default is 0

  Notes   : The -start argument only applies when -orf is set to 1. By 
default
            all initiation codons found in the given codon table are used
            but when "start" is set to some codon this codon will be used
            exclusively as the initiation codon. Note that the default codon
            table (NCBI "Standard") has 3 initiation codons!

            By default translate() translates termination codons to
            the some character (default is *), both internal and trailing
            codons. Setting "-complete" to 1 tells translate() to remove
            the trailing character.

		   -offset is used for seqfeatures which contain the the \codon_start
		   tag and can be set to 1, 2, or 3.  This is the offset by which the
		   sequence translation starts relative to the first base of the
		   feature

For details on codon tables used by translate() see 
L<Bio::Tools::CodonTable>.

            Deprecated argument set (v. 1.5.1 and prior versions)
            where each argument is an element in an array:

            1: character for terminator (optional), defaults to '*'.
            2: character for unknown amino acid (optional), defaults to 'X'.
            3: frame (optional), valid values are 0, 1, 2, defaults to 0.
            4: codon table id (optional), defaults to 1.
            5: complete coding sequence expected, defaults to 0 (false).
            6: boolean, throw exception if not complete coding sequence
               (true), defaults to warning (false)
            7: codontable, a custom Bio::Tools::CodonTable object 
(optional).

=cut

And here's what appears on CPAN:

Title   : translate
  Usage   : $protein_seq_obj = $dna_seq_obj->translate

  Function:

            Provides the translation of the DNA sequence using full
            IUPAC ambiguities in DNA/RNA and amino acid codes.

            The full CDS translation is identical to EMBL/TREMBL
            database translation. Note that the trailing terminator
            character is removed before returning the translation
            object.

            Note: if you set $dna_seq_obj->verbose(1) you will get a
            warning if the first codon is not a valid initiator.


  Returns : A Bio::PrimarySeqI implementing object
  Args    : character for terminator (optional) defaults to '*'
            character for unknown amino acid (optional) defaults to 'X'
            frame (optional) valid values 0, 1, 2, defaults to 0
            codon table id (optional) defaults to 1
            complete coding sequence expected, defaults to 0 (false)
            boolean, throw exception if not complete CDS (true) or 
defaults to warning (false)

Most of the POD is missing - does anyone know why?

Brian O.

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