Bio::DB::DBFetch(3) User Contributed Perl Documentation Bio::DB::DBFetch(3)NAMEBio::DB::DBFetch - Database object for retrieving using the dbfetch
script
SYNOPSIS
#do not use this module directly
DESCRIPTION
Allows the dynamic retrieval of entries from databases using the
dbfetch script at EBI: http://www.ebi.ac.uk/cgi-bin/dbfetch.
In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out. This allows later
additions of more servers in different geographical locations.
This is a superclass which is called by instantiable subclasses with
correct parameters.
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 - Heikki Lehvaslaiho
Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Routines from Bio::DB::WebDBSeqI
get_request
Title : get_request
Usage : my $url = $self->get_request
Function: returns a HTTP::Request object
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
postprocess_data
Title : postprocess_data
Usage : $self->postprocess_data ( 'type' => 'string',
'location' => \$datastr);
Function: process downloaded data before loading into a Bio::SeqIO
Returns : void
Args : hash with two keys - 'type' can be 'string' or 'file'
- 'location' either file location or string
reference containing data
default_format
Title : default_format
Usage : my $format = $self->default_format
Function: Returns default sequence format for this module
Returns : string
Args : none
Bio::DB::DBFetch specific routines
get_Stream_by_id
Title : get_Stream_by_id
Usage : $seq = $db->get_Stream_by_id($ref);
Function: Retrieves Seq objects from the server 'en masse', rather than one
at a time. For large numbers of sequences, this is far superior
than get_Stream_by_[id/acc]().
Example :
Returns : a Bio::SeqIO stream object
Args : $ref : either an array reference, a filename, or a filehandle
from which to get the list of unique ids/accession numbers.
NOTE: for backward compatibility, this method is also called
get_Stream_by_batch.
get_Seq_by_version
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : version number (as a string)
Throws : "version does not exist" exception
request_format
Title : request_format
Usage : my ($req_format, $ioformat) = $self->request_format;
$self->request_format("genbank");
$self->request_format("fasta");
Function: Get/Set sequence format retrieval. The get-form will normally not
be used outside of this and derived modules.
Returns : Array of two strings, the first representing the format for
retrieval, and the second specifying the corresponding SeqIO format.
Args : $format = sequence format
servertype
Title : servertype
Usage : my $servertype = $self->servertype
$self->servertype($servertype);
Function: Get/Set server type
Returns : string
Args : server type string [optional]
hostlocation
Title : hostlocation
Usage : my $location = $self->hostlocation()
$self->hostlocation($location)
Function: Set/Get Hostlocation
Returns : string representing hostlocation
Args : string specifying hostlocation [optional]
location_url
Title : location
Usage : my $url = $self->location_url()
Function: Get host url
Returns : string representing url
Args : none
Bio::DB::DBFetch routines
These methods allow subclasses to pass parameters.
hosts
Title : hosts
Usage :
Function: get/set for host hash
Returns :
Args : optional hash
formatmap
Title : formatmap
Usage :
Function: get/set for format hash
Returns :
Args : optional hash
perl v5.14.1 2011-07-22 Bio::DB::DBFetch(3)
