/ 
bioperl-0.7.2
/ Bio::DB::GenPept

NAME

Bio::DB::GenPept - Database object interface to GenPept

SYNOPSIS

    $gb = new Bio::DB::GenPept;

    $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";
    }

DESCRIPTION

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).

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/MailList.shtml  - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Aaron Mackey, Jason Stajich

Email amackey@virginia.edu Email jason@chg.mc.duke.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get_params

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

default_format

Title   : default_format
Usage   : my $format = $self->default_format
Function: Returns default sequence format for this module
Returns : string
Args    : none

Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI

get_Seq_by_id

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

get_Seq_by_acc

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 retrive by

Routines implemented by Bio::DB::NCBIHelper

get_request

Title   : get_request
Usage   : my $url = $self->get_request
Function: HTTP::Request
Returns : 
Args    : %qualifiers = a hash of qualifiers (ids, format, etc)

get_Stream_by_batch

Title   : get_Stream_by_batch
Usage   : $seq = $db->get_Stream_by_batch($ref);
Function: Retrieves Seq objects from Entrez '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.

get_Stream_by_id

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

get_Stream_by_acc (2)

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()

request_format

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