Optional functions

_show_dna()

(output only) shows the dna or not

_post_sort()

(output only) provides a sorting func which is applied to the FTHelpers before printing

_id_generation_func()

This is function which is called as

   print "ID   ", $func($annseq), "\n";
    

To generate the ID line. If it is not there, it generates a sensible ID line using a number of tools.

If you want to output annotations in EMBL format they need to be stored in a Bio::Annotation::Collection object which is accessible through the Bio::SeqI interface method annotation().

The following are the names of the keys which are polled from a Bio::Annotation::Collection object.

 reference  - Should contain Bio::Annotation::Reference objects
 comment    - Should contain Bio::Annotation::Comment objects
 dblink     - Should contain Bio::Annotation::DBLink objects
    

Mailing Lists

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

  https://github.com/bioperl/bioperl-live/issues

next_seq

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    :

_write_ID_line

 Title   : _write_ID_line
 Usage   : $self->_write_ID_line($seq);
 Function: Writes the EMBL Release 87 format ID line to the stream, unless
         : there is a user-supplied ID line generation function in which
         : case that is used instead.
         : ( See Bio::SeqIO::embl::_id_generation_function(). )
 Returns : nothing
 Args    : Bio::Seq object

_is_valid_division

 Title   : _is_valid_division
 Usage   : $self->_is_valid_division($div)
 Function: tests division code for validity
 Returns : true if $div is a valid EMBL release 87 taxonomic division.
 Args    : taxonomic division code string

_is_valid_molecule_type

 Title   : _is_valid_molecule_type
 Usage   : $self->_is_valid_molecule_type($mol)
 Function: tests molecule type for validity
 Returns : true if $mol is a valid EMBL release 87 molecule type.
 Args    : molecule type string

write_seq

 Title   : write_seq
 Usage   : $stream->write_seq($seq)
 Function: writes the $seq object (must be seq) to the stream
 Returns : 1 for success and undef for error
 Args    : array of 1 to n Bio::SeqI objects

_print_EMBL_FTHelper

 Title   : _print_EMBL_FTHelper
 Usage   :
 Function: Internal function
 Returns : 1 if writing succeeded, otherwise undef
 Args    :

_read_EMBL_Contig()

 Title   : _read_EMBL_Contig
 Usage   : 
 Function: convert CO lines into annotations
 Returns : 
 Args    :

_read_EMBL_References

 Title   : _read_EMBL_References
 Usage   :
 Function: Reads references from EMBL format. Internal function really
 Example :
 Returns :
 Args    :

_read_EMBL_Species

 Title   : _read_EMBL_Species
 Usage   :
 Function: Reads the EMBL Organism species and classification
           lines.
 Example :
 Returns : A Bio::Species object
 Args    : a reference to the current line buffer, accession number

_read_EMBL_DBLink

 Title   : _read_EMBL_DBLink
 Usage   :
 Function: Reads the EMBL database cross reference ("DR") lines
 Example :
 Returns : A list of Bio::Annotation::DBLink objects
 Args    :

_read_EMBL_TaxID_DBLink

 Title   : _read_EMBL_TaxID_DBLink
 Usage   :
 Function: Reads the EMBL database cross reference to NCBI TaxID ("OX") lines
 Example :
 Returns : A list of Bio::Annotation::DBLink objects
 Args    :

_filehandle

 Title   : _filehandle
 Usage   : $obj->_filehandle($newval)
 Function:
 Example :
 Returns : value of _filehandle
 Args    : newvalue (optional)

_read_FTHelper_EMBL

 Title   : _read_FTHelper_EMBL
 Usage   : _read_FTHelper_EMBL($buffer)
 Function: reads the next FT key line
 Example :
 Returns : Bio::SeqIO::FTHelper object
 Args    : filehandle and reference to a scalar

_write_line_EMBL

 Title   : _write_line_EMBL
 Usage   :
 Function: internal function
 Example :
 Returns : 1 if writing succeeded, else undef
 Args    :

_write_line_EMBL_regex

 Title   : _write_line_EMBL_regex
 Usage   :
 Function: internal function for writing lines of specified
           length, with different first and the next line
           left hand headers and split at specific points in the
           text
 Example :
 Returns : nothing
 Args    : file handle, first header, second header, text-line, regex for line breaks, total line length

_post_sort

 Title   : _post_sort
 Usage   : $obj->_post_sort($newval)
 Function:
 Returns : value of _post_sort
 Args    : newvalue (optional)

_show_dna

 Title   : _show_dna
 Usage   : $obj->_show_dna($newval)
 Function:
 Returns : value of _show_dna
 Args    : newvalue (optional)

_id_generation_func

 Title   : _id_generation_func
 Usage   : $obj->_id_generation_func($newval)
 Function:
 Returns : value of _id_generation_func
 Args    : newvalue (optional)

_ac_generation_func

 Title   : _ac_generation_func
 Usage   : $obj->_ac_generation_func($newval)
 Function:
 Returns : value of _ac_generation_func
 Args    : newvalue (optional)

_sv_generation_func

 Title   : _sv_generation_func
 Usage   : $obj->_sv_generation_func($newval)
 Function:
 Returns : value of _sv_generation_func
 Args    : newvalue (optional)

_kw_generation_func

 Title   : _kw_generation_func
 Usage   : $obj->_kw_generation_func($newval)
 Function:
 Returns : value of _kw_generation_func
 Args    : newvalue (optional)