NAME¶
Bio::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 'Unpublished (2003)',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:
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
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