—————#
# bioperl module for FAST::Bio::SeqFeature::Tools::IDHandler
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Mungall <cjm@fruitfly.org>
#
# Copyright Chris Mungall
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::SeqFeature::Tools::IDHandler - maps $seq_feature-E<gt>primary_tag
=head1 SYNOPSIS
use FAST::Bio::SeqIO;
use FAST::Bio::SeqFeature::Tools::IDHandler;
=head1 DESCRIPTION
Class to map $seq_feature-E<gt>primary_tag
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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:
=head1 AUTHOR - Chris Mungall
Email: cjm@fruitfly.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
use
strict;
# Object preamble - inherits from FAST::Bio::Root::Root
=head2 new
Title : new
Usage : $unflattener = FAST::Bio::SeqFeature::Tools::IDHandler->new();
Function: constructor
Example :
Returns : a new FAST::Bio::SeqFeature::Tools::IDHandler
Args : see below
=cut
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!
}
=head2 set_ParentIDs_from_hierarchy()
Title : set_ParentIDs_from_hierarchy()
Usage : $idhandler->set_ParentIDs_from_hierarchy($fholder)
Function: populates tags Parent and ID via holder hierarchy
Example :
Returns :
Args : FAST::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
=cut
# method author: cjm@fruitfly.org
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
;
}
=head2 create_hierarchy_from_ParentIDs
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 :
=cut
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
;
}
=head2 generate_unique_persistent_id
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, B<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
=cut
# method author: cjm@fruitfly.org
sub
generate_unique_persistent_id{
my
(
$self
,
$sf
,
@args
) =
@_
;
my
$id
;
if
(!
$sf
->isa(
"FAST::Bio::SeqFeatureI"
)) {
$sf
->throw(
"not a FAST::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;