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