| Bio::DB::DBFetch(3pm) | User Contributed Perl Documentation | Bio::DB::DBFetch(3pm) |
Bio::DB::DBFetch - Database object for retrieving using the dbfetch script
#do not use this module directly
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.
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
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.
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
Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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)
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
Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none
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.
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : version number (as a string)
Throws : "version does not exist" exception
Title : request_format
Usage : my ($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
Title : servertype
Usage : my $servertype = $self->servertype
$self->servertype($servertype);
Function: Get/Set server type
Returns : string
Args : server type string [optional]
Title : hostlocation
Usage : my $location = $self->hostlocation()
$self->hostlocation($location)
Function: Set/Get Hostlocation
Returns : string representing hostlocation
Args : string specifying hostlocation [optional]
Title : location Usage : my $url = $self->location_url() Function: Get host url Returns : string representing url Args : none
These methods allow subclasses to pass parameters.
Title : hosts Usage : Function: get/set for host hash Returns : Args : optional hash
Title : formatmap Usage : Function: get/set for format hash Returns : Args : optional hash
| 2021-08-15 | perl v5.32.1 |