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   ", $func($seq), "\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 Genbank 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 pulled from a Bio::Annotation::Collection object:

 reference       - Should contain Bio::Annotation::Reference objects
 comment         - Should contain Bio::Annotation::Comment objects
 dblink          - Should contain a Bio::Annotation::DBLink object
 segment         - Should contain a Bio::Annotation::SimpleValue object
 origin          - Should contain a Bio::Annotation::SimpleValue object
 wgs             - Should contain a Bio::Annotation::SimpleValue object
    

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_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 0 for error
 Args    : array of 1 to n Bio::SeqI objects

_print_GenBank_FTHelper¶

 Title   : _print_GenBank_FTHelper
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

_read_GenBank_References¶

 Title   : _read_GenBank_References
 Usage   :
 Function: Reads references from GenBank format. Internal function really
 Returns :
 Args    :

_add_ref_to_array¶

Title: _add_ref_to_array Usage: Function: Adds a Reference object to an array of Reference objects, takes
care of possible cleanups to be done (currently, only author and title
will be chopped of trailing semicolons). Args: A reference to an array of Reference objects and
the Reference object to be added Returns: nothing

_read_GenBank_Species¶

 Title   : _read_GenBank_Species
 Usage   :
 Function: Reads the GenBank Organism species and classification
           lines. Able to deal with unconvential Organism naming
           formats, and varietas in plants
 Example : ORGANISM  unknown marine gamma proteobacterium NOR5
           $genus = undef
           $species = unknown marine gamma proteobacterium NOR5
           ORGANISM  Drosophila sp. 'white tip scutellum'
           $genus = Drosophila
           $species = sp. 'white tip scutellum'
           (yes, this really is a species and that is its name)
           $subspecies = undef
           ORGANISM  Ajellomyces capsulatus var. farciminosus
           $genus = Ajellomyces
           $species = capsulatus
           $subspecies = var. farciminosus
           ORGANISM  Hepatitis delta virus
           $genus = undef (though this virus has a genus in its lineage, we
                           cannot know that without a database lookup)
           $species = Hepatitis delta virus
 Returns : A Bio::Species object
 Args    : A reference to the current line buffer

_read_FTHelper_GenBank¶

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

_write_line_GenBank¶

 Title   : _write_line_GenBank
 Usage   :
 Function: internal function
 Example :
 Returns :
 Args    :

_write_line_GenBank_regex¶

 Title   : _write_line_GenBank_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)