Bio::DB::GenPept.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

     $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";
     }
 
 

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/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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.

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 the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Aaron Mackey, Jason Stajich

Email amackey@virginia.edu Email jason@bioperl.org

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_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