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
<
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://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 : 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. 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)