| Bio::SeqFeature::Tools::TypeMapper(3pm) | User Contributed Perl Documentation | Bio::SeqFeature::Tools::TypeMapper(3pm) |
Bio::SeqFeature::Tools::TypeMapper - maps $seq_feature->primary_tag
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);
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.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
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
Email: cjm@fruitfly.org
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(); Function: constructor Example : Returns : a new Bio::SeqFeature::Tools::TypeMapper Args : see below
Title : typemap Usage : $obj->typemap($newval) Function: Example : Returns : value of typemap (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : map_types Usage : Function: Example : Returns : Args : dgg: added -undefined => "region" option to produce all valid SO mappings.
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);
}
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
| 2021-08-15 | perl v5.32.1 |