/ 
bioperl-0.6
/ 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('195055'); # Accession Number

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.

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.

vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented discussion
http://bio.perl.org/MailList.html             - 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

Email amackey@virginia.edu

APPENDIX

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

get_Seq_by_id

Title   : get_Seq_by_id
Usage   : $seq = $db->get_Seq_by_id($uid);
Function: Gets a Bio::Seq object by its unique identifier/name
Returns : a Bio::Seq object
Args    : $uid : the id (as a string) of the desired sequence entry

get_Seq_by_acc

Title   : get_Seq_by_acc
Usage   : $seq = $db->get_Seq_by_acc($acc);
Function: Gets a Bio::Seq object by its accession number
Returns : a Bio::Seq object
Args    : $acc : the accession number of the desired sequence entry
Note    : For GenPept, this just calls the same code for get_Seq_by_id()

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

Title   : get_Stream_by_acc
Usage   : $seq = $db->get_Seq_by_acc($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 GenPept, this just calls the same code for get_Stream_by_id()

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 id's/accession numbers.