| Bio::DB::GenPept(3pm) | User Contributed Perl Documentation | Bio::DB::GenPept(3pm) |
Bio::DB::GenPept - Database object interface to GenPept
$gb = Bio::DB::GenPept->new();
$seq = $gb->get_Seq_by_id('195055'); # Unique ID
# or ...
$seq = $gb->get_Seq_by_acc('DEECTH'); # Accession Number
my $seqio = $gb->get_Stream_by_id(['195055', 'DEECTH']);
while( my $seq = $seqio->next_seq ) {
print "seq is is ", $seq->display_id, "\n";
}
Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the GenPept database at NCBI, via an Entrez query.
WARNING: Please do NOT spam the Entrez web server with multiple requests. NCBI offers Batch Entrez for this purpose. Batch Entrez support will likely be supported in a future version of DB::GenPept.
Currently the only return format supported by NCBI Entrez for GenPept database is GenPept format, so any format specification passed to GenPept will be ignored still be forced to GenPept format (which is just GenBank format).
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 amackey@virginia.edu Email jason@bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_params
Usage : my %params = $self->get_params($mode)
Function: Returns key,value pairs to be passed to NCBI database
for either 'batch' or 'single' sequence retrieval method
Returns : a key,value pair hash
Args : 'single' or 'batch' mode for retrieval
Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none
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('AAC73346');
Function: Gets a Seq objects by accession number
Returns : Bio::Seq object
Args : accession number to retrieve by
Title : get_request Usage : my $url = $self->get_request Function: HTTP::Request Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc)
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_acc
Usage : $seq = $db->get_Stream_by_acc($acc);
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 : request_format
Usage : my $format = $self->request_format;
$self->request_format($format);
Function: Get/Set sequence format retrieval
Returns : string representing format
Args : $format = sequence format
| 2018-10-27 | perl v5.26.2 |