Manual Reference Pages - BIO::SEQFEATURE::TOOLS::TYPEMAPPER (3)
Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature->primary_tag
# first fetch a genbank SeqI object
$seq = $seqio->next_seq();
$tm = Bio::SeqFeature::Tools::TypeMapper->new;
# map all the types in the sequence
my $f = shift;
$f->length > 1 ?
variation : SNP
# alternatively, use the hardcoded SO mapping
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.
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.
firstname.lastname@example.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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AUTHOR - Chris Mungall
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Title : new
Usage : $unflattener = Bio::SeqFeature::Tools::TypeMapper->new();
Returns : a new Bio::SeqFeature::Tools::TypeMapper
Args : see below
Title : typemap
Usage : $obj->typemap($newval)
Returns : value of typemap (a scalar)
Args : on set, new value (a scalar or undef, optional)
Title : map_types
dgg: added -undefined => "region" option to produce all valid SO mappings.
Title : map_types_to_SO
hardcodes the genbank to SO mapping
Based on revision 1.22 of SO
Please see the actual code for the mappings
dgg: separated out FT_SO_map for caller changes. Update with:
open(FTSO,"curl -s http://sequenceontology.org/resources/mapping/FT_SO.txt|");
chomp; ($ft,$so,$sid,$ftdef,$sodef)= split"\t";
print " $ft => $so,\n" if($ft && $so && $ftdef);
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
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 <B>part_ofB>. 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
In chado speak, the child is the <B>subjectB> feature and the parent is
the <B>objectB> feature
|perl v5.20.3 ||BIO::SEQFEATURE::TOOLS::TYPEMAPPER (3) ||2016-04-05 |
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