Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::ClusterIO - Handler for Cluster Formats


         #NB: This example is unigene specific

         use Bio::ClusterIO;

         $stream  = Bio::ClusterIO->new('-file' => "",
                                        '-format' => "unigene");
         # note: we quote -format to keep older perl's from complaining.

         while ( my $in = $stream->next_cluster() ) {
             print $in->unigene_id() . "\n";
             while ( my $sequence = $in->next_seq() ) {
                 print $sequence->accession_number() . "\n";
         # Parsing errors are printed to STDERR.


       The ClusterIO module works with the ClusterIO format module to read various cluster
       formats such as NCBI UniGene.


          $str = Bio::ClusterIO->new(-file => 'filename',

       The new() class method constructs a new Bio::ClusterIO object.  The returned object can be
       used to retrieve or print cluster objects. new() accepts the following parameters:

           A file path to be opened for reading.

           Specify the format of the file.  Supported formats include:

              unigene              *.data  UniGene build files.
              dbsnp                *.xml   dbSNP XML files

           If no format is specified and a filename is given, then the module will attempt to
           deduce it from the filename.  If this is unsuccessful, the main UniGene build format
           is assumed.

           The format name is case insensitive.  'UNIGENE', 'UniGene' and 'unigene' are all
           supported, as are dbSNP, dbsnp, and DBSNP


       See below for more detailed summaries.  The main methods are:

   $cluster = $str->next_cluster()
       Fetch the next cluster from the stream.

       These I've left in here because they were in the SeqIO module. Feedback appreciated. There
       they provide the tie interface.  See perltie for more details.


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AUTHOR - Andrew Macgregor



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

        Title   : new
        Usage   : Bio::ClusterIO->new(-file => $filename, -format => 'format')
        Function: Returns a new cluster stream
        Returns : A Bio::ClusterIO::Handler initialised with the appropriate format
        Args    : -file => $filename
                  -format => format

        Title   : format
        Usage   : $format = $stream->format()
        Function: Get the cluster format
        Returns : cluster format
        Args    : none

        Title   : next_cluster
        Usage   : $cluster = $stream->next_cluster()
        Function: Reads the next cluster object from the stream and returns it.
        Returns : a L<Bio::ClusterI> compliant object
        Args    : none

        Title   : cluster_factory
        Usage   : $obj->cluster_factory($newval)
        Function: Get/set the object factory to use for creating the cluster
        Example :
        Returns : a L<Bio::Factory::ObjectFactoryI> compliant object
        Args    : on set, new value (a L<Bio::Factory::ObjectFactoryI>
                  compliant object or undef, optional)

        Title   : object_factory
        Usage   : $obj->object_factory($newval)
        Function: This is an alias to cluster_factory with a more generic name.
        Example :
        Returns : a L<Bio::Factory::ObjectFactoryI> compliant object
        Args    : on set, new value (a L<Bio::Factory::ObjectFactoryI>
                  compliant object or undef, optional)

        Title   : _load_format_module
        Usage   : *INTERNAL ClusterIO stuff*
        Function: Loads up (like use) a module at run time on demand
        Example :
        Returns :
        Args    :

        Title   : _guess_format
        Usage   : $obj->_guess_format($filename)
        Function: guess format based on file suffix
        Example :
        Returns : guessed format of filename (lower case)
        Args    :
        Notes   : formats that _filehandle() will guess include unigene and dbsnp