Bio::SeqIO::gbdriver(3User Contributed Perl DocumentatiBio::SeqIO::gbdriver(3)NAMEBio::SeqIO::gbdriver - GenBank handler-based push parser
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 => 'gbdriver');
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. The key difference between this parser and the tried-
and-true Bio::SeqIO::genbank parser is this version separates the
parsing and data manipulation into a 'driver' method (next_seq) and
separate object handlers which deal with the data passed to it.
The Driver
The main purpose of the driver routine, in this case next_seq(), is to
carve out the data into meaningful chunks which are passed along to
relevant handlers (see below).
Each chunk of data in the has a NAME tag attached to it, similar to
that for XML parsing. This designates the type of data passed
(annotation type or seqfeature) and the handler to be called for
processing the data.
For GenBank annotations, the data is divided up and passed along to
handlers according to whether the data is tagged with a field name
(i.e. LOCUS) and whether the field name represents 'primary' annotation
(in this case, is present at the beginning of the line, such as
REFERENCE). If the field is primary, it is assigned to the NAME tag.
Field names which aren't primary (have at least 2 spaces before the
name, like ORGANISM) are appended to the preceding primary field name
as additional tags.
For feature table data each new feature name signals the beginning of a
new chunk of data. 'FEATURES' is attached to NAME, the feature key
('CDS', 'gene', etc) is attached as the PRIMARY_ID, and the location is
assigned to it's own tag name (LOCATION). Feature qualifiers are added
as additional keys, with multiple keys included in an array.
Once a particular event occurs (new primary tag, sequence, end of
record), the data is passed along to be processed by a handler or (if
no handler is defined) tossed away.
Internally, the hash ref for a representative annotation (here a
REFERENCE) looks like this:
$VAR1 = {
'JOURNAL' => 'Unpublished (2003)',
'TITLE' => 'The DNA sequence of Homo sapiens',
'NAME' => 'REFERENCE',
'REFERENCE' => '1 (bases 1 to 10001)',
'AUTHORS' => 'International Human Genome Sequencing Consortium.'
};
and a SeqFeature as this:
$VAR1 = {
'db_xref' => [
'GeneID:127086',
'InterimID:127086'
],
'LOCATION' => 'complement(3024..6641)',
'NAME' => 'FEATURES',
'FEATURE_KEY' => 'gene',
'gene' => 'LOC127086',
'note' => 'Derived by automated computational analysis using
gene prediction method: GNOMON.'
};
Note that any driver implementation would suffice as long as it
fulfilled the requirements above.
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:
http://bugzilla.open-bio.org/
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
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
seqhandler
Title : seqhandler
Usage : $stream->seqhandler($handler)
Function: Get/Set teh Bio::Seq::HandlerBaseI object
Returns : Bio::Seq::HandlerBaseI
Args : Bio::Seq::HandlerBaseI
perl v5.14.1 2011-07-22 Bio::SeqIO::gbdriver(3)
