Bio::SeqFeature::Tools IDHandler
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Summary
Bio::SeqFeature::Tools::IDHandler - maps $seq_feature->primary_tag
Package variables
No package variables defined.
Inherit
Bio::Root::Root
Synopsis
  use Bio::SeqIO;
use Bio::SeqFeature::Tools::IDHandler;
Description
Class to map $seq_feature->primary_tag
Methods
newDescriptionCode
set_ParentIDs_from_hierarchy()
No description
Code
create_hierarchy_from_ParentIDsDescriptionCode
generate_unique_persistent_idDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : $unflattener = Bio::SeqFeature::Tools::IDHandler->new();
Function: constructor
Example :
Returns : a new Bio::SeqFeature::Tools::IDHandler
Args : see below
create_hierarchy_from_ParentIDscodeprevnextTop
 Title   : create_hierarchy_from_ParentIDs
Usage : $idhandler->set_ParentIDs_from_hierarchy($fholder)
Function: inverse of set_ParentIDs_from_hierarchy
Example :
Returns : list of top SeqFeatures
Args :
generate_unique_persistent_idcodeprevnextTop
 Title   : generate_unique_persistent_id
Usage :
Function: generates a unique and persistent identifier for this
Example :
Returns : value of primary_id (a scalar)
Args :
Will generate an ID, and set primary_id() (see above)
The ID is a string generated from
  seq_id
primary_tag
start
end
There are three underlying assumptions: that all the above accessors
are set; that seq_id is a persistent and unique identifier for the
sequence containing this feature; and that
  (seq_id, primary_tag, start, end) 
is a "unique constraint" over features
The ID is persistent, so long as none of these values change - if they
do, it is considered a separate entity
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    my($generate_id_sub) =
	$self->_rearrange([qw(GENERATE_ID_SUB
			     )],
                          @args);

    return $self; # success - we hope!
}
set_ParentIDs_from_hierarchy()descriptionprevnextTop
sub set_ParentIDs_from_hierarchy() {
   my $self = shift;
   my ($featholder) = @_;

   # we will traverse the tree of contained seqfeatures
# (a seqfeature is itself a holder)
# start with the top-level features
my @sfs = $featholder->get_SeqFeatures; # clear existing parent tags
# (we assume this is the desired behaviour)
my @all_sfs = $featholder->get_all_SeqFeatures; foreach (@all_sfs) { if ($_->has_tag('Parent')) { $_->remove_tag('Parent'); } } # iterate until entire tree traversed
while (@sfs) { my $sf = shift @sfs; my @subsfs = $sf->get_SeqFeatures; # see if the ID tag
my $id = $sf->primary_id; if (!$id) { # the skolem function feature(seq,start,end,type)
# is presumed to uniquely identify this feature, and
# to also be persistent
$id = $sf->generate_unique_persistent_id; } foreach my $subsf (@subsfs) { $subsf->add_tag_value('Parent', $id); } # push children on to end of stack (breadth first search)
push(@sfs, @subsfs); } return;
}
create_hierarchy_from_ParentIDsdescriptionprevnextTop
sub create_hierarchy_from_ParentIDs {
   my ($self,$featholder,@args) = @_;

   my @sfs = $featholder->get_all_SeqFeatures;
   my %sf_by_ID = ();
   foreach (@sfs) {
       my $id = $_->primary_id;
       next unless $id;
       if ($sf_by_ID{$id}) {
           $featholder->throw("DUPLICATE ID: $id");
       }
       $sf_by_ID{$id} = $_;
       $_->remove_SeqFeatures; # clear existing hierarchy (assume this is desired)
} if (!%sf_by_ID) { # warn??
# this is actually expected behaviour for some kinds of data;
# eg lists of STSs - no containment hierarchy
return; } my @topsfs = grep { my @parents = $_->get_tagset_values('Parent'); foreach my $parent (@parents) { $sf_by_ID{$parent}->add_SeqFeature($_) if exists $sf_by_ID{$parent}; } !@parents; } @sfs; $featholder->remove_SeqFeatures; $featholder->add_SeqFeature($_) foreach @topsfs; return @topsfs;
}
generate_unique_persistent_iddescriptionprevnextTop
sub generate_unique_persistent_id {
   my ($self,$sf,@args) = @_;

   my $id;
   if (!$sf->isa("Bio::SeqFeatureI")) {
       $sf->throw("not a Bio::SeqFeatureI");
   }
   my $seq_id = $sf->seq_id || $sf->throw("seq_id must be set: ".$sf->display_name);
   #my $seq_id = $sf->seq_id || 'unknown_seq';
if ($sf->has_tag('transcript_id')) { ($id) = $sf->get_tag_values('transcript_id'); } elsif ($sf->has_tag('protein_id')) { ($id) = $sf->get_tag_values('protein_id'); } else { my $source = $sf->source_tag || $sf->throw("source tag must be set: ".$sf->display_name); #my $source = $sf->source_tag || 'unknown_source';
my $start = $sf->start || $sf->throw("start must be set or is zero: ".$sf->display_name); my $end = $sf->end || $sf->throw("end must be set"); my $type = $sf->primary_tag || $sf->throw("primary_tag/type must be set: ".$sf->display_name); $id = "$source:$type:$seq_id:$start:$end"; } $sf->primary_id($id); return $id; } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris MungallTop
Email: cjm@fruitfly.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
set_ParentIDs_from_hierarchy()Top
 Title   : set_ParentIDs_from_hierarchy()
Usage : $idhandler->set_ParentIDs_from_hierarchy($fholder)
Function: populates tags Parent and ID via holder hierarchy
Example :
Returns :
Args : Bio::featureHolderI (either a SeqFeature or a Seq)
This is mainly for GFF3 export
GFF3 uses the tags ID and Parent to represent the feature containment
hierarchy; it does NOT use the feature holder tree
This method sets Parent (and ID for any parents not set) based on
feature holder/containement hierarchy, ready for GFF3 output