Bio::SeqFeature::Tools::TypeMapper man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

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:

	 http://bugzilla.open-bio.org/

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 v5.14.1			  2011-07Bio::SeqFeature::Tools::TypeMapper(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net