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)