NAME¶

Bio::Factory::SequenceProcessorI - Interface for chained sequence
processing algorithms

SYNOPSIS¶

    use Bio::SeqIO;
    use MySeqProcessor; # is-a Bio::Factory::SequenceProcessorI
    # obtain your source stream, e.g., an EMBL file
    my $seqin = Bio::SeqIO->new(-fh => \*STDIN, -format => 'embl');
    # create your processor (it must implement this interface)
    my $seqalgo = MySeqProcessor->new();
    # chain together
    $seqalgo->source_stream($seqin);
    # you could create more processors and chain them one after another
    # ...
    # finally, the last link in the chain is your SeqIO stream
    my $seqpipe = $seqalgo;
    # once you've established the pipeline, proceed as if you had a
    # single SeqIO stream
    while(my $seq = $seqpipe->next_seq()) {
        # ... do something ...
    }

DESCRIPTION¶

This defines an interface that allows seamless chaining of sequence processing algorithms encapsulated in modules while retaining the overall Bio::SeqIO interface at the end of the pipeline.

This is especially useful if you want an easily configurable processing pipeline of re-usable algorithms as building blocks instead of (hard-)coding the whole algorithm in a single script.

There are literally no restrictions as to what an individual module can do with a sequence object it obtains from the source stream before it makes it available through its own next_seq() method. It can manipulate the sequence object, but otherwise keep it intact, but it can also create any number of new sequence objects from it, or it can discard some, or any combination thereof. The only requirement is that its next_seq() method return Bio::PrimarySeqI compliant objects. In order to play nice, if a processor creates new objects it should try to use the same sequence factory that the source stream uses, but this is not strongly mandated.

FEEDBACK¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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

AUTHOR - Hilmar Lapp¶

Email hlapp at gmx.net

APPENDIX¶

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

 Title   : source_stream
 Usage   : $obj->source_stream($newval)
 Function: Get/set the source sequence stream for this sequence
           processor.
           An implementation is not required to allow set, but will
           usually do so.
 Example : 
 Returns : A Bio::Factory::SequenceStreamI compliant object
 Args    : on set, new value (a Bio::Factory::SequenceStreamI compliant
           object)

Bio::Factory::SequenceStreamI methods¶

 The requirement to implement these methods is inherited from
 L<Bio::Factory::SequenceStreamI>. An implementation may not
 necessarily have to implement all methods in a meaningful way. Which
 methods will be necessary very much depends on the context in which
 an implementation of this interface is used. E.g., if it is only used
 for post-processing sequences read from a SeqIO stream, write_seq()
 will not be used and hence does not need to be implemented in a
 meaningful way (it may in fact even throw an exception).
 Also, since an implementor will already receive built objects from a
 sequence stream, sequence_factory() may or may not be relevant,
 depending on whether the processing method does or does not involve
 creating new objects.

 Title   : next_seq
 Usage   : $seq = stream->next_seq
 Function: Reads the next sequence object from the stream and returns it.
           In the case of a non-recoverable situation an exception
           will be thrown.  Do not assume that you can resume parsing
           the same stream after catching the exception. Note that you
           can always turn recoverable errors into exceptions by
           calling $stream->verbose(2).
 Returns : a Bio::Seq sequence object
 Args    : none

 Title   : write_seq
 Usage   : $stream->write_seq($seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Seq object

 Title   : sequence_factory
 Usage   : $seqio->sequence_factory($seqfactory)
 Function: Get the Bio::Factory::SequenceFactoryI
 Returns : Bio::Factory::SequenceFactoryI
 Args    : none