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¶

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

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

Support¶

Please direct usage questions or support issues to the mailing list:

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¶

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  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)