| Bio::DB::BioFetch(3pm) | User Contributed Perl Documentation | Bio::DB::BioFetch(3pm) |
Bio::DB::BioFetch - Database object interface to BioFetch retrieval
use Bio::DB::BioFetch;
$bf = Bio::DB::BioFetch->new();
$seq = $bf->get_Seq_by_id('HSFOS'); # EMBL or SWALL ID
# change formats, storage procedures
$bf = Bio::DB::BioFetch->new(-format => 'fasta',
-retrievaltype => 'tempfile',
-db => 'EMBL');
$stream = $bf->get_Stream_by_id(['HSFOS','J00231']);
while (my $s = $stream->next_seq) {
print $s->seq,"\n";
}
# get a RefSeq entry
$bf->db('refseq');
eval {
$seq = $bf->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION
};
print "accession is ", $seq->accession_number, "\n" unless $@;
Bio::DB::BioFetch is a guaranteed best effort sequence entry fetching method. It goes to the Web-based dbfetch server located at the EBI (http://www.ebi.ac.uk/Tools/dbfetch/dbfetch) to retrieve sequences in the EMBL or GenBank sequence repositories.
This module implements all the Bio::DB::RandomAccessI interface, plus the get_Stream_by_id() and get_Stream_by_acc() methods that are found in the Bio::DB::SwissProt interface.
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 Lincoln Stein <lstein@cshl.org<
Also thanks to Heikki Lehvaslaiho <heikki-at-bioperl-dot-org> for the BioFetch server and interface specification.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $bf = Bio::DB::BioFetch->new(@args) Function: Construct a new Bio::DB::BioFetch object Returns : a Bio::DB::BioFetch object Args : see below Throws :
@args are standard -name=>value options as listed in the following table. If you do not provide any options, the module assumes reasonable defaults.
Option Value Default
------ ----- -------
-baseaddress location of dbfetch server http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
-retrievaltype "tempfile" or "io_string" io_string
-format "embl", "fasta", "swissprot", embl
or "genbank"
-db "embl", "genbank" or "swissprot" embl
Title : new_from_registry Usage : $biofetch = $db->new_from_registry(%config) Function: Creates a BioFetch object from the registry config hash Returns : itself Args : A configuration hash (see Registry.pm) Throws :
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object
Args : the id (as a string) of a sequence
Throws : "id does not exist" exception
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
Title : get_Seq_by_gi
Usage : $seq = $db->get_Seq_by_gi('405830');
Function: Gets a Bio::Seq object by gi number
Returns : A Bio::Seq object
Args : gi number (as a string)
Throws : "gi does not exist" exception
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by sequence version
Returns : A Bio::Seq object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
Title : get_Stream_by_id
Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] );
Function: Gets a series of Seq objects by unique identifiers
Returns : a Bio::SeqIO stream object
Args : $ref : a reference to an array of unique identifiers for
the desired sequence entries
Title : get_Stream_by_gi
Usage : $seq = $db->get_Seq_by_gi([$gi1, $gi2]);
Function: Gets a series of Seq objects by gi numbers
Returns : a Bio::SeqIO stream object
Args : $ref : a reference to an array of gi numbers for
the desired sequence entries
Note : For GenBank, this just calls the same code for get_Stream_by_id()
Title : get_Stream_by_batch
Usage : $seq = $db->get_Stream_by_batch($ref);
Function: Get a series of Seq objects by their IDs
Example :
Returns : a Bio::SeqIO stream object
Args : $ref : an array reference containing a list of unique
ids/accession numbers.
In some of the Bio::DB::* moduels, get_Stream_by_id() is called get_Stream_by_batch(). Since there seems to be no consensus, this is provided as an alias.
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 : default_format Usage : $format = $self->default_format Function: return the default format Returns : a string Args :
Title : default_db Usage : $db = $self->default_db Function: return the default database Returns : a string Args :
Title : db Usage : $db = $self->db([$db]) Function: get/set the database Returns : a string Args : new database
Title : postprocess_data
Usage : $self->postprocess_data ( 'type' => 'string',
'location' => \$datastr);
Function: process downloaded data before loading into a Bio::SeqIO
Returns : void
Args : hash with two keys - 'type' can be 'string' or 'file'
- 'location' either file location or string
reference containing data
Title : request_format
Usage : my ($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
Overriding WebDBSeqI method to help newbies to retrieve sequences. EMBL database is all too often passed RefSeq accessions. This redirects those calls. See Bio::DB::RefSeq.
Title : get_Stream_by_acc
Usage : $seq = $db->get_Seq_by_acc([$acc1, $acc2]);
Function: Gets a series of Seq objects by accession numbers
Returns : a Bio::SeqIO stream object
Args : $ref : a reference to an array of accession numbers for
the desired sequence entries
Title : _check_id
Usage :
Function: Throw on whole chromosome NCBI sequences not in sequence databases
and redirect RefSeq accession requests sent to EMBL.
Returns :
Args : $id(s), $string
Throws : if accessionn number indicates whole chromosome NCBI sequence
| 2018-10-27 | perl v5.26.2 |