| Bio::DB::EMBL(3pm) | User Contributed Perl Documentation | Bio::DB::EMBL(3pm) |
Bio::DB::EMBL - Database object interface for EMBL entry retrieval
use Bio::DB::EMBL;
$embl = Bio::DB::EMBL->new();
# remember that EMBL_ID does not equal GenBank_ID!
$seq = $embl->get_Seq_by_id('HSFOS'); # EMBL ID
print "cloneid is ", $seq->id, "\n";
# or changeing to accession number and Fasta format ...
$embl->request_format('fasta');
$seq = $embl->get_Seq_by_acc('J02231'); # EMBL ACC
print "cloneid is ", $seq->id, "\n";
# especially when using versions, you better be prepared
# in not getting what what want
eval {
$seq = $embl->get_Seq_by_version('J02231.1'); # EMBL VERSION
};
print "cloneid is ", $seq->id, "\n" unless $@;
# or ... best when downloading very large files, prevents
# keeping all of the file in memory
# also don't want features, just sequence so let's save bandwidth
# and request Fasta sequence
$embl = Bio::DB::EMBL->new(-retrievaltype => 'tempfile' ,
-format => 'fasta');
my $seqio = $embl->get_Stream_by_id(['AC013798', 'AC021953'] );
while( my $clone = $seqio->next_seq ) {
print "cloneid is ", $clone->id, "\n";
}
Allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL database using the dbfetch script at EBI: <http://www.ebi.ac.uk/Tools/dbfetch/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.
The functionality of this module is inherited from Bio::DB::DBFetch which implements Bio::DB::WebDBSeqI.
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 : new Usage : $gb = Bio::DB::GenBank->new(@options) Function: Creates a new genbank handle Returns : New genbank handle Args : -delay number of seconds to delay between fetches (3s)
NOTE: There are other options that are used internally.
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
Note : For GenBank, this just calls the same code for get_Stream_by_id()
Title : _check_id Usage : Function: Returns : A Bio::DB::RefSeq reference or throws Args : $id(s), $string
| 2018-10-27 | perl v5.26.2 |