#
# bioperl module for Bio::Coordinate::Pair
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Coordinate::Pair - Continuous match between two coordinate sets
=head1 SYNOPSIS
use Bio::Location::Simple;
use Bio::Coordinate::Pair;
my $match1 = Bio::Location::Simple->new
(-seq_id => 'propeptide', -start => 21, -end => 40, -strand=>1 );
my $match2 = Bio::Location::Simple->new
(-seq_id => 'peptide', -start => 1, -end => 20, -strand=>1 );
my $pair = Bio::Coordinate::Pair->new(-in => $match1,
-out => $match2
);
# location to match
$pos = Bio::Location::Simple->new
(-start => 25, -end => 25, -strand=> -1 );
# results are in a Bio::Coordinate::Result
# they can be Matches and Gaps; are Bio::LocationIs
$res = $pair->map($pos);
$res->isa('Bio::Coordinate::Result');
$res->each_match == 1;
$res->each_gap == 0;
$res->each_Location == 1;
$res->match->start == 5;
$res->match->end == 5;
$res->match->strand == -1;
$res->match->seq_id eq 'peptide';
=head1 DESCRIPTION
This class represents a one continuous match between two coordinate
systems represented by Bio::Location::Simple objects. The relationship
is directed and reversible. It implements methods to ensure internal
consistency, and map continuous and split locations from one
coordinate system to another.
The map() method returns Bio::Coordinate::Results with
Bio::Coordinate::Result::Gaps. The calling code have to deal (process
or ignore) them.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Heikki Lehvaslaiho
Email: heikki-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Coordinate::Pair;
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Coordinate::Result;
use Bio::Coordinate::Result::Match;
use Bio::Coordinate::Result::Gap;
use base qw(Bio::Root::Root Bio::Coordinate::MapperI);
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my($in, $out) =
$self->_rearrange([qw(IN
OUT
)],
@args);
$in && $self->in($in);
$out && $self->out($out);
return $self; # success - we hope!
}
=head2 in
Title : in
Usage : $obj->in('peptide');
Function: Set and read the input coordinate system.
Example :
Returns : value of input system
Args : new value (optional), Bio::LocationI
=cut
sub in {
my ($self,$value) = @_;
if( defined $value) {
$self->throw("Not a valid input Bio::Location [$value] ")
unless $value->isa('Bio::LocationI');
$self->{'_in'} = $value;
}
return $self->{'_in'};
}
=head2 out
Title : out
Usage : $obj->out('peptide');
Function: Set and read the output coordinate system.
Example :
Returns : value of output system
Args : new value (optional), Bio::LocationI
=cut
sub out {
my ($self,$value) = @_;
if( defined $value) {
$self->throw("Not a valid output coordinate Bio::Location [$value] ")
unless $value->isa('Bio::LocationI');
$self->{'_out'} = $value;
}
return $self->{'_out'};
}
=head2 swap
Title : swap
Usage : $obj->swap;
Function: Swap the direction of mapping; input <-> output
Example :
Returns : 1
Args :
=cut
sub swap {
my ($self) = @_;
($self->{'_in'}, $self->{'_out'}) = ($self->{'_out'}, $self->{'_in'});
return 1;
}
=head2 strand
Title : strand
Usage : $obj->strand;
Function: Get strand value for the pair
Example :
Returns : ( 1 | 0 | -1 )
Args :
=cut
sub strand {
my ($self) = @_;
$self->warn("Outgoing coordinates are not defined")
unless $self->out;
$self->warn("Incoming coordinates are not defined")
unless $self->in;
return ($self->in->strand || 0) * ($self->out->strand || 0);
}
=head2 test
Title : test
Usage : $obj->test;
Function: test that both components are of the same length
Example :
Returns : ( 1 | undef )
Args :
=cut
sub test {
my ($self) = @_;
$self->warn("Outgoing coordinates are not defined")
unless $self->out;
$self->warn("Incoming coordinates are not defined")
unless $self->in;
return ($self->in->end - $self->in->start) == ($self->out->end - $self->out->start);
}
=head2 map
Title : map
Usage : $newpos = $obj->map($pos);
Function: Map the location from the input coordinate system
to a new value in the output coordinate system.
Example :
Returns : new Bio::LocationI in the output coordinate system or undef
Args : Bio::LocationI object
=cut
sub map {
my ($self,$value) = @_;
$self->throw("Need to pass me a value.")
unless defined $value;
$self->throw("I need a Bio::Location, not [$value]")
unless $value->isa('Bio::LocationI');
$self->throw("Input coordinate system not set")
unless $self->in;
$self->throw("Output coordinate system not set")
unless $self->out;
if ($value->isa("Bio::Location::SplitLocationI")) {
my $result = Bio::Coordinate::Result->new();
foreach my $loc ( $value->sub_Location(1) ) {
my $res = $self->_map($loc);
map { $result->add_sub_Location($_) } $res->each_Location;
}
return $result;
} else {
return $self->_map($value);
}
}
=head2 _map
Title : _map
Usage : $newpos = $obj->_map($simpleloc);
Function: Internal method that does the actual mapping. Called
multiple times by map() if the location to be mapped is a
split location
Example :
Returns : new location in the output coordinate system or undef
Args : Bio::Location::Simple
=cut
sub _map {
my ($self,$value) = @_;
my $result = Bio::Coordinate::Result->new();
my $offset = $self->in->start - $self->out->start;
my $start = $value->start - $offset;
my $end = $value->end - $offset;
my $match = Bio::Location::Simple->new;
$match->location_type($value->location_type);
$match->strand($self->strand);
#within
# |-------------------------|
# |-|
if ($start >= $self->out->start and $end <= $self->out->end) {
$match->seq_id($self->out->seq_id);
$result->seq_id($self->out->seq_id);
if ($self->strand >= 0) {
$match->start($start);
$match->end($end);
} else {
$match->start($self->out->end - $end + $self->out->start);
$match->end($self->out->end - $start + $self->out->start);
}
if ($value->strand) {
$match->strand($match->strand * $value->strand);
$result->strand($match->strand);
}
bless $match, 'Bio::Coordinate::Result::Match';
$result->add_sub_Location($match);
}
#out
# |-------------------------|
# |-| or |-|
elsif ( ($end < $self->out->start or $start > $self->out->end ) or
#insertions just outside the range need special settings
($value->location_type eq 'IN-BETWEEN' and
($end = $self->out->start or $start = $self->out->end))) {
$match->seq_id($self->in->seq_id);
$result->seq_id($self->in->seq_id);
$match->start($value->start);
$match->end($value->end);
$match->strand($value->strand);
bless $match, 'Bio::Coordinate::Result::Gap';
$result->add_sub_Location($match);
}
#partial I
# |-------------------------|
# |-----|
elsif ($start < $self->out->start and $end <= $self->out->end ) {
$result->seq_id($self->out->seq_id);
if ($value->strand) {
$match->strand($match->strand * $value->strand);
$result->strand($match->strand);
}
my $gap = Bio::Location::Simple->new;
$gap->start($value->start);
$gap->end($self->in->start - 1);
$gap->strand($value->strand);
$gap->seq_id($self->in->seq_id);
bless $gap, 'Bio::Coordinate::Result::Gap';
$result->add_sub_Location($gap);
# match
$match->seq_id($self->out->seq_id);
if ($self->strand >= 0) {
$match->start($self->out->start);
$match->end($end);
} else {
$match->start($self->out->end - $end + $self->out->start);
$match->end($self->out->end);
}
bless $match, 'Bio::Coordinate::Result::Match';
$result->add_sub_Location($match);
}
#partial II
# |-------------------------|
# |------|
elsif ($start >= $self->out->start and $end > $self->out->end ) {
$match->seq_id($self->out->seq_id);
$result->seq_id($self->out->seq_id);
if ($value->strand) {
$match->strand($match->strand * $value->strand);
$result->strand($match->strand);
}
if ($self->strand >= 0) {
$match->start($start);
$match->end($self->out->end);
} else {
$match->start($self->out->start);
$match->end($self->out->end - $start + $self->out->start);
}
bless $match, 'Bio::Coordinate::Result::Match';
$result->add_sub_Location($match);
my $gap = Bio::Location::Simple->new;
$gap->start($self->in->end + 1);
$gap->end($value->end);
$gap->strand($value->strand);
$gap->seq_id($self->in->seq_id);
bless $gap, 'Bio::Coordinate::Result::Gap';
$result->add_sub_Location($gap);
}
#enveloping
# |-------------------------|
# |---------------------------------|
elsif ($start < $self->out->start and $end > $self->out->end ) {
$result->seq_id($self->out->seq_id);
if ($value->strand) {
$match->strand($match->strand * $value->strand);
$result->strand($match->strand);
}
# gap1
my $gap1 = Bio::Location::Simple->new;
$gap1->start($value->start);
$gap1->end($self->in->start - 1);
$gap1->strand($value->strand);
$gap1->seq_id($self->in->seq_id);
bless $gap1, 'Bio::Coordinate::Result::Gap';
$result->add_sub_Location($gap1);
# match
$match->seq_id($self->out->seq_id);
$match->start($self->out->start);
$match->end($self->out->end);
bless $match, 'Bio::Coordinate::Result::Match';
$result->add_sub_Location($match);
# gap2
my $gap2 = Bio::Location::Simple->new;
$gap2->start($self->in->end + 1);
$gap2->end($value->end);
$gap2->strand($value->strand);
$gap2->seq_id($self->in->seq_id);
bless $gap2, 'Bio::Coordinate::Result::Gap';
$result->add_sub_Location($gap2);
} else {
$self->throw("Should not be here!");
}
return $result;
}
1;