/ 
bioperl-1.2.2
/ 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 system. Go:

    $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 alot of flexibility here about how to dump things which I need to document fully.

Mapping of record properties to object properties

This section is supposed to document which sections and properties of a GenBank databank record end up where in the Bioperl object model. It is far from complete and presently focuses only on those mappings which may be non-obvious. $seq in the text refers to the Bio::Seq::RichSeqI implementing object returned by the parser for each record.

GI number

$seq->primary_id

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 polled from a Bio::Annotation::Collection object.

reference - Should contain Bio::Annotation::Reference objects comment - Should contain Bio::Annotation::Comment objects

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://www.bioperl.org/MailList.shtml  - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR - Elia Stupka

Email elia@tll.org.sg

CONTRIBUTORS

Ewan Birney birney@ebi.ac.uk Jason Stajich jason@bioperl.org Chris Mungall cjm@fruitfly.bdgp.berkeley.edu Lincoln Stein lstein@cshl.org Heikki Lehvaslaiho, heikki@ebi.ac.uk Hilmar Lapp, hlapp@gmx.net Donald G. Jackson, donald.jackson@bms.com

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    :

_read_GenBank_Species

Title   : _read_GenBank_Species
Usage   :
Function: Reads the GenBank Organism species and classification
          lines.
Example :
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)