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Manual Reference Pages  -  BIO::DB::GENPEPT (3)

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NAME

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

CONTENTS

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:



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



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



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perl v5.20.3 BIO::DB::GENPEPT (3) 2016-04-05

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