NAME
FAST::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 = FAST::Bio::SeqIO->new(-file => $filename,
-format => 'GenBank');
while ( my $seq = $stream->next_seq() ) {
# do something with $seq
}DESCRIPTION
This object can transform FAST::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 FAST::Bio::Annotation::Collection object which is accessible through the FAST::Bio::SeqI interface method annotation().
The following are the names of the keys which are pulled from a FAST::Bio::Annotation::Collection object:
reference - Should contain FAST::Bio::Annotation::Reference objects comment - Should contain FAST::Bio::Annotation::Comment objects dblink - Should contain a FAST::Bio::Annotation::DBLink object segment - Should contain a FAST::Bio::Annotation::SimpleValue object origin - Should contain a FAST::Bio::Annotation::SimpleValue object wgs - Should contain a FAST::Bio::Annotation::SimpleValue object
Where does the data go?
Data parsed in FAST::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 FAST::Bio::AnnotationCollectionI object which is associated with FAST::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 listsSupport
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://redmine.open-bio.org/projects/bioperl/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 : FAST::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 FAST::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. 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)
$species = Hepatitis delta virus
Returns : A FAST::Bio::Species object
Args : A reference to the current line buffer_read_FTHelper_GenBank
Title : _read_FTHelper_GenBank
Usage : _read_FTHelper_GenBank($buffer)
Function: reads the next FT key line
Example :
Returns : FAST::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)