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BioPerl-1.007000_006
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SeqIO::genbank

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 contruct 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.open-bio.org/wiki/HOWTO:Feature-Annotation.

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)