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Bio::SeqFeature::ToolsUserpContributed PeBio::SeqFeature::Tools::TypeMapper(3)

NAME
       Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature->primary_tag

SYNOPSIS
	 use Bio::SeqIO;
	 use Bio::SeqFeature::Tools::TypeMapper;

	 # first fetch a genbank SeqI object
	 $seqio	=
	   Bio::SeqIO->new(-file=>'AE003644.gbk',
			   -format=>'GenBank');
	 $seq =	$seqio->next_seq();

	 $tm = Bio::SeqFeature::Tools::TypeMapper->new;

	 # map all the types in	the sequence
	 $tm->map_types(-seq=>$seq,
			{CDS=>'ORF',
			 variation=>sub	{
			     my	$f = shift;
			     $f->length	> 1 ?
			       'variation' : 'SNP'
			 },
			});

	  # alternatively, use the hardcoded SO	mapping
	  $tm->map_types_to_SO(-seq=>$seq);

DESCRIPTION
       This class implements an	object for mapping between types; for example,
       the types in a genbank feature table, and the types specified in	the
       Sequence	Ontology.

       You can specify your own	mapping, either	as a simple hash index,	or by
       providing your own subroutines.

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 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 - Chris Mungall
       Email:  cjm@fruitfly.org

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

   new
	Title	: new
	Usage	: $unflattener = Bio::SeqFeature::Tools::TypeMapper->new();
	Function: constructor
	Example	:
	Returns	: a new	Bio::SeqFeature::Tools::TypeMapper
	Args	: see below

   typemap
	Title	: typemap
	Usage	: $obj->typemap($newval)
	Function:
	Example	:
	Returns	: value	of typemap (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   map_types
	Title	: map_types
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

	dgg: added -undefined => "region" option to produce all	valid SO mappings.

   map_types_to_SO
	Title	: map_types_to_SO
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

       hardcodes the genbank to	SO mapping

       Based on	revision 1.22 of SO

       Please see the actual code for the mappings

       Taken from

       <http://sequenceontology.org/resources/mapping/FT_SO.txt>

       dgg: separated out FT_SO_map for	caller changes.	Update with:

	 open(FTSO,"curl -s http://sequenceontology.org/resources/mapping/FT_SO.txt|");
	 while(<FTSO>){
	   chomp; ($ft,$so,$sid,$ftdef,$sodef)=	split"\t";
	   print "     '$ft' =>	'$so',\n" if($ft && $so	&& $ftdef);
	 }

   get_relationship_type_by_parent_child
	Title	: get_relationship_type_by_parent_child
	Usage	: $type	= $tm->get_relationship_type_by_parent_child($parent_sf, $child_sf);
	Usage	: $type	= $tm->get_relationship_type_by_parent_child('mRNA', 'protein');
	Function: given	two features where the parent contains the child,
		  will determine what the relationship between them in
	Example	:
	Returns	:
	Args	: parent SeqFeature, child SeqFeature OR
		  parent type string, child type string	OR

       bioperl Seq::FeatureHolderI hierarchies are equivalent to unlabeled
       graphs (where parent nodes are the containers, and child	nodes are the
       features	being contained). For example, a feature of type mRNA can
       contain features	of type	exon.

       Some external representations (eg chadoxml or chaosxml) require that
       the edges in the	feature	relationship graph are labeled.	For example,
       the type	between	mRNA and exon would be part_of.	Although it stretches
       the bioperl notion of containment, we could have	a CDS contained	by an
       mRNA (for example, the Bio::SeqFeature::Tools::Unflattener module takes
       genbank records and makes these kind of links. The relationship here
       would be	produced_by

       In chado	speak, the child is the	subject	feature	and the	parent is the
       object feature

perl v5.24.1			  2017-07Bio::SeqFeature::Tools::TypeMapper(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chris Mungall | APPENDIX

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