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

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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 email or the web: bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/ Email hlapp at gmx.net Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

source_stream
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) 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.

next_seq
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 See Bio::Root::RootI

write_seq
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

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