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Bio::ClusterIO(3)     User Contributed Perl Documentation    Bio::ClusterIO(3)

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

perl v5.24.1			  2017-07-08		     Bio::ClusterIO(3)

NAME | SYNOPSIS | DESCRIPTION | CONSTRUCTORS | OBJECT METHODS | FEEDBACK | AUTHOR - Andrew Macgregor | APPENDIX

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