Reference

Bio::DB::GenPept(3pm)

Database object interface to GenPept

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('P09651.5'); # Accession Number
    my $seqio = $gb->get_Stream_by_id(['195055', 'P09651.5']);
    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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Aaron Mackey, Jason Stajich

Email [email protected] Email [email protected]

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('P09651.5')
 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 retrieve 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()

get_Stream_by_query

  Title   : get_Stream_by_query
  Usage   : $seq = $db->get_Stream_by_query('ROA1_HUMAN');
  Function: Gets a series of Seq objects by unique display_id
  Returns : a Bio::SeqIO stream object
  Args    : $ref : display_id to query by

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

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