Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::SeqIO::genbank - GenBank sequence input/output stream

SYNOPSIS

       It is probably best not to use this object directly, but rather go through the SeqIO
       handler:

           $stream = Bio::SeqIO->new(-file   => $filename,
                                     -format => 'GenBank');

           while ( my $seq = $stream->next_seq ) {
               # do something with $seq
           }

DESCRIPTION

       This object can transform Bio::Seq objects to and from GenBank flat file databases.

       There is some flexibility here about how to write GenBank output that is not fully
       documented.

   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

Where does the data go?

       Data parsed in Bio::SeqIO::genbank is stored in a variety of data fields in the sequence
       object that is returned. Here is a partial list of fields.

       Items listed as RichSeq or Seq or PrimarySeq and then NAME() tell you the top level object
       which defines a function called NAME() which stores this information.

       Items listed as Annotation 'NAME' tell you the data is stored the associated
       Bio::AnnotationCollectionI object which is associated with Bio::Seq objects.  If it is
       explicitly requested that no annotations should be stored when parsing a record of course
       they will not be available when you try and get them.  If you are having this problem look
       at the type of SeqBuilder that is being used to construct your sequence object.

        Comments             Annotation 'comment'
        References           Annotation 'reference'
        Segment              Annotation 'segment'
        Origin               Annotation 'origin'
        Dbsource             Annotation 'dblink'

        Accessions           PrimarySeq accession_number()
        Secondary accessions RichSeq get_secondary_accessions()
        GI number            PrimarySeq primary_id()
        LOCUS                PrimarySeq display_id()
        Keywords             RichSeq get_keywords()
        Dates                RichSeq get_dates()
        Molecule             RichSeq molecule()
        Seq Version          RichSeq seq_version()
        PID                  RichSeq pid()
        Division             RichSeq division()
        Features             Seq get_SeqFeatures()
        Alphabet             PrimarySeq alphabet()
        Definition           PrimarySeq description() or desc()
        Version              PrimarySeq version()

        Sequence             PrimarySeq seq()

       There is more information in the Feature-Annotation HOWTO about each field and how it is
       mapped to the Sequence object
       <http://bioperl.org/howtos/Features_and_Annotations_HOWTO.html>.

FEEDBACK

   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

AUTHOR - Bioperl Project

       bioperl-l at bioperl.org

       Original author Elia Stupka, elia -at- tigem.it

CONTRIBUTORS

       Ewan Birney birney at ebi.ac.uk Jason Stajich jason at bioperl.org Chris Mungall cjm at
       fruitfly.bdgp.berkeley.edu Lincoln Stein lstein at cshl.org Heikki Lehvaslaiho, heikki at
       ebi.ac.uk Hilmar Lapp, hlapp at gmx.net Donald G. Jackson, donald.jackson at bms.com James
       Wasmuth, james.wasmuth at ed.ac.uk Brian Osborne, bosborne at alum.mit.edu Chris Fields,
       cjfields at bioperl dot org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   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)