Bio::DB::HIV::HIVAnnotProcessor.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

HIVAnnotProcessor - Adds HIV-specific annotations to Bio::SeqIO streams

SYNOPSIS

    sub get_Stream_by_query {
        my ($self, $query ) = @_;
        my $stream = $self->get_seq_stream('-query' => $query, '-mode'=>'query');
        return new Bio::DB::HIV::HIVAnnotProcessor( -hiv_query=>$query, 
                                                    -source_stream=>$stream );
    }
 
 

DESCRIPTION

Bio::DB::HIV::HIVAnnotProcessor is chained to the "next_seq" of a sequence stream returned from a query to the Los Alamos HIV sequence database made using Bio::DB::HIV and Bio::DB::Query::HIVQuery. It adds the annotations obtained in the "Bio::DB::Query::HIVQuery" to the Bio::Seq objects themselves via the "$seq->annotation" method.

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Mark A. Jensen

Email maj@fortinbras.us

CONTRIBUTORS

Mark A. Jensen

APPENDIX

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

Constructor

new

  Title   : new
  Usage   : my $obj = new HIVAnnotProcessor();
  Function: Builds a new HIVAnnotProcessor object 
  Returns : an instance of HIVAnnotProcessor
  Args    :
 
 

Bio::Factory::SequenceProcessorI compliance

source_stream

  Title   : source_stream
  Usage   : $hap->source_stream($newval)
  Function: 
  Example : 
  Returns : value of source_stream (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

next_seq

  Title   : next_seq
  Usage   : $seqobj = stream->next_seq
  Function: Reads the next sequence object from the stream, 
          : adds annotations from the HIVQuery object according
          : to the sequence id, and returns sequence object
  Returns : a Bio::Seq sequence object
  Args    : none
 
 

write_seq

  Title   : write_seq
  Usage   : $seqobj->write_seq
  Function: for HIVAnnotProcessor, throw an exception
  Example :
  Returns : Bio::Root::IOException
  Args    :
 
 

HIVAnnotProcessor-specific methods

hiv_query

  Title   : hiv_query
  Usage   : $obj->hiv_query($newval)
  Function: 
  Example : 
  Returns : value of hiv_query (a Bio::DB::Query::HIVQuery object)
  Args    : on set, new value (an HIVQuery object, optional)