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

NAME

       Bio::ClusterIO - Handler for Cluster Formats

SYNOPSIS

         #NB: This example is unigene specific

         use Bio::ClusterIO;

         $stream  = Bio::ClusterIO->new('-file' => "Hs.data",
                                        '-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.

DESCRIPTION

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

CONSTRUCTORS

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

       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:

       -file
           A file path to be opened for reading.

       -format
           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

OBJECT METHODS

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

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

   TIEHANDLE(), READLINE(), PRINT()
       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.

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 - Andrew Macgregor

       Email andrew@anatomy.otago.ac.nz

APPENDIX

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

   new
        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

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

   next_cluster
        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

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

   object_factory
        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)

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

   _guess_format
        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