|-file||A file path to be opened for reading.|
Specify the format of the file. Supported formats include:
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:
CW$cluster = CW$str->next_cluster()Fetch the next cluster from the stream.
TIEHANDLE(), READLINE(), PRINT()These Ive 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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Please direct usage questions or support issues to the mailing list:
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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 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)
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
|perl v5.20.3||BIO::CLUSTERIO (3)||2016-04-05|