[Bioperl-l] What is CPAN doing?

[Brian Osborne]

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.