#
# bioperl module for Bio::Coordinate::GeneMapper
#
# 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::GeneMapper - transformations between gene related coordinate systems
=head1 SYNOPSIS
use Bio::Coordinate::GeneMapper;
# get a Bio::RangeI representing the start, end and strand of the CDS
# in chromosomal (or entry) coordinates
my $cds;
# get a Bio::Location::Split or an array of Bio::LocationI objects
# holding the start, end and strand of all the exons in chromosomal
# (or entry) coordinates
my $exons;
# create a gene mapper and set it to map from chromosomal to cds coordinates
my $gene = Bio::Coordinate::GeneMapper->new(-in =>'chr',
-out =>'cds',
-cds =>$cds,
-exons=>$exons
);
# get a a Bio::Location or sequence feature in input (chr) coordinates
my $loc;
# map the location into output coordinates and get a new location object
$newloc = $gene->map($loc);
=head1 DESCRIPTION
Bio::Coordinate::GeneMapper is a module for simplifying the mappings
of coodinate locations between various gene related locations in human
genetics. It also adds a special human genetics twist to coordinate
systems by making it possible to disable the use of zero
(0). Locations before position one start from -1. See method
L<nozero>.
It understands by name the following coordinate systems and mapping
between them:
peptide (peptide length)
^
| -peptide_offset
|
frame propeptide (propeptide length)
^ ^
\ |
translate \ |
\ |
cds (transcript start and end)
^
negative_intron | \
^ | \ transcribe
\ | \
intron exon \
^ ^ ^ /
splice \ \ / | /
\ \ / | /
\ inex | /
\ ^ | /
\ \ |/
----- gene (gene_length)
^
| - gene_offset
|
chr (or entry)
This structure is kept in the global variable $DAG which is a
representation of a Directed Acyclic Graph. The path calculations
traversing this graph are done in a helper class. See
L<Bio::Coordinate::Graph>.
Of these, two operations are special cases, translate and splice.
Translating and reverse translating are implemented as internal
methods that do the simple 1E<lt>-E<gt>3 conversion. Splicing needs
additional information that is provided by method L<exons> which takes
in an array of Bio::LocationI objects.
Most of the coordinate system names should be selfexplanatory to
anyone familiar with genes. Negative intron coordinate system is
starts counting backwards from -1 as the last nucleotide in the
intron. This used when only exon and a few flanking intron nucleotides
are known.
This class models coordinates within one transcript of a gene, so to
tackle multiple transcripts you need several instances of the
class. It is therefore valid to argue that the name of the class
should be TranscriptMapper. GeneMapper is a catchier name, so it
stuck.
=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::GeneMapper;
use vars qw(%COORDINATE_SYSTEMS %COORDINATE_INTS $TRANSLATION $DAG
$NOZERO_VALUES $NOZERO_KEYS);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Coordinate::Result;
use Bio::Location::Simple;
use Bio::Coordinate::Graph;
use Bio::Coordinate::Collection;
use Bio::Coordinate::Pair;
use Bio::Coordinate::ExtrapolatingPair;
use base qw(Bio::Root::Root Bio::Coordinate::MapperI);
# first set internal values for all translation tables
%COORDINATE_SYSTEMS = (
peptide => 10,
propeptide => 9,
frame => 8,
cds => 7,
negative_intron => 6,
intron => 5,
exon => 4,
inex => 3,
gene => 2,
chr => 1
);
%COORDINATE_INTS = (
10 => 'peptide',
9 => 'propeptide',
8 => 'frame',
7 => 'cds',
6 => 'negative_intron',
5 => 'intron',
4 => 'exon',
3 => 'inex',
2 => 'gene',
1 => 'chr'
);
$TRANSLATION = $COORDINATE_SYSTEMS{'cds'}. "-".
$COORDINATE_SYSTEMS{'propeptide'};
$DAG = {
10 => [],
9 => [10],
8 => [],
7 => [8, 9],
6 => [],
5 => [6],
4 => [7],
3 => [4, 5],
2 => [3, 4, 5, 7],
1 => [2]
};
$NOZERO_VALUES = {0 => 0, 'in' => 1, 'out' => 2, 'in&out' => 3 };
$NOZERO_KEYS = { 0 => 0, 1 => 'in', 2 => 'out', 3 => 'in&out' };
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
# prime the graph
my $graph = Bio::Coordinate::Graph->new();
$graph->hash_of_arrays($DAG);
$self->graph($graph);
my($in, $out, $peptide_offset, $exons,
$cds, $nozero, $strict) =
$self->_rearrange([qw(IN
OUT
PEPTIDE_OFFSET
EXONS
CDS
NOZERO
STRICT
)],
@args);
# direction of mapping when going chr to protein
$self->{_direction} = 1;
$in && $self->in($in);
$out && $self->out($out);
$cds && $self->cds($cds);
$exons && ref($exons) =~ /ARRAY/i && $self->exons(@$exons);
$peptide_offset && $self->peptide_offset($peptide_offset);
$nozero && $self->nozero($nozero);
$strict && $self->strict($strict);
return $self; # success - we hope!
}
=head2 in
Title : in
Usage : $obj->in('peptide');
Function: Set and read the input coordinate system.
Example :
Returns : value of input system
Args : new value (optional)
=cut
sub in {
my ($self,$value) = @_;
if( defined $value) {
$self->throw("Not a valid input coordinate system name [$value]\n".
"Valid values are ". join(", ", keys %COORDINATE_SYSTEMS ))
unless defined $COORDINATE_SYSTEMS{$value};
$self->{'_in'} = $COORDINATE_SYSTEMS{$value};
}
return $COORDINATE_INTS{ $self->{'_in'} };
}
=head2 out
Title : out
Usage : $obj->out('peptide');
Function: Set and read the output coordinate system.
Example :
Returns : value of output system
Args : new value (optional)
=cut
sub out {
my ($self,$value) = @_;
if( defined $value) {
$self->throw("Not a valid input coordinate system name [$value]\n".
"Valid values are ". join(", ", keys %COORDINATE_SYSTEMS ))
unless defined $COORDINATE_SYSTEMS{$value};
$self->{'_out'} = $COORDINATE_SYSTEMS{$value};
}
return $COORDINATE_INTS{ $self->{'_out'} };
}
=head2 strict
Title : strict
Usage : $obj->strict('peptide');
Function: Set and read whether strict boundaried of coordinate
systems are enforced.
When strict is on, the end of the coordinate range must be defined.
Example :
Returns : boolean
Args : boolean (optional)
=cut
sub strict {
my ($self,$value) = @_;
if( defined $value) {
$value ? ( $self->{'_strict'} = 1 ) : ( $self->{'_strict'} = 0 );
## update in each mapper !!
}
return $self->{'_strict'} || 0 ;
}
=head2 nozero
Title : nozero
Usage : $obj->nozero(1);
Function: Flag to disable the use of zero in the input,
output or both coordinate systems. Use of coordinate
systems without zero is a peculiarity common in
human genetics community.
Example :
Returns : 0 (default), or 'in', 'out', 'in&out'
Args : 0 (default), or 'in', 'out', 'in&out'
=cut
sub nozero {
my ($self,$value) = @_;
if (defined $value) {
$self->throw("Not a valid value for nozero [$value]\n".
"Valid values are ". join(", ", keys %{$NOZERO_VALUES} ))
unless defined $NOZERO_VALUES->{$value};
$self->{'_nozero'} = $NOZERO_VALUES->{$value};
}
my $res = $self->{'_nozero'} || 0;
return $NOZERO_KEYS->{$res};
}
=head2 graph
Title : graph
Usage : $obj->graph($new_graph);
Function: Set and read the graph object representing relationships
between coordinate systems
Example :
Returns : Bio::Coordinate::Graph object
Args : new Bio::Coordinate::Graph object (optional)
=cut
sub graph {
my ($self,$value) = @_;
if( defined $value) {
$self->throw("Not a valid graph [$value]\n")
unless $value->isa('Bio::Coordinate::Graph');
$self->{'_graph'} = $value;
}
return $self->{'_graph'};
}
=head2 peptide
Title : peptide
Usage : $obj->peptide_offset($peptide_coord);
Function: Read and write the offset of peptide from the start of propeptide
and peptide length
Returns : a Bio::Location::Simple object
Args : a Bio::LocationI object
=cut
sub peptide {
my ($self, $value) = @_;
if( defined $value) {
$self->throw("I need a Bio::LocationI, not [". $value. "]")
unless $value->isa('Bio::LocationI');
$self->throw("Peptide start not defined")
unless defined $value->start;
$self->{'_peptide_offset'} = $value->start - 1;
$self->throw("Peptide end not defined")
unless defined $value->end;
$self->{'_peptide_length'} = $value->end - $self->{'_peptide_offset'};
my $a = $self->_create_pair
('propeptide', 'peptide', $self->strict,
$self->{'_peptide_offset'}, $self->{'_peptide_length'} );
my $mapper = $COORDINATE_SYSTEMS{'propeptide'}. "-". $COORDINATE_SYSTEMS{'peptide'};
$self->{'_mappers'}->{$mapper} = $a;
}
return Bio::Location::Simple->new
(-seq_id => 'propeptide',
-start => $self->{'_peptide_offset'} + 1 ,
-end => $self->{'_peptide_length'} + $self->{'_peptide_offset'},
-strand => 1,
-verbose => $self->verbose,
);
}
=head2 peptide_offset
Title : peptide_offset
Usage : $obj->peptide_offset(20);
Function: Set and read the offset of peptide from the start of propeptide
Returns : set value or 0
Args : new value (optional)
=cut
sub peptide_offset {
my ($self,$offset, $len) = @_;
if( defined $offset) {
$self->throw("I need an integer, not [$offset]")
unless $offset =~ /^[+-]?\d+$/;
$self->{'_peptide_offset'} = $offset;
if (defined $len) {
$self->throw("I need an integer, not [$len]")
unless $len =~ /^[+-]?\d+$/;
$self->{'_peptide_length'} = $len;
}
my $a = $self->_create_pair
('propeptide', 'peptide', $self->strict, $offset, $self->{'_peptide_length'} );
my $mapper = $COORDINATE_SYSTEMS{'propeptide'}. "-". $COORDINATE_SYSTEMS{'peptide'};
$self->{'_mappers'}->{$mapper} = $a;
}
return $self->{'_peptide_offset'} || 0;
}
=head2 peptide_length
Title : peptide_length
Usage : $obj->peptide_length(20);
Function: Set and read the offset of peptide from the start of propeptide
Returns : set value or 0
Args : new value (optional)
=cut
sub peptide_length {
my ($self, $len) = @_;
if( defined $len) {
$self->throw("I need an integer, not [$len]")
if defined $len && $len !~ /^[+-]?\d+$/;
$self->{'_peptide_length'} = $len;
}
return $self->{'_peptide_length'};
}
=head2 exons
Title : exons
Usage : $obj->exons(@exons);
Function: Set and read the offset of CDS from the start of transcript
You do not have to sort the exons before calling this method as
they will be sorted automatically.
If you have not defined the CDS, is will be set to span all
exons here.
Returns : array of Bio::LocationI exons in genome coordinates or 0
Args : array of Bio::LocationI exons in genome (or entry) coordinates
=cut
sub exons {
my ($self,@value) = @_;
my $cds_mapper = $COORDINATE_SYSTEMS{'gene'}. "-". $COORDINATE_SYSTEMS{'cds'};
my $inex_mapper =
$COORDINATE_SYSTEMS{'gene'}. "-". $COORDINATE_SYSTEMS{'inex'};
my $exon_mapper =
$COORDINATE_SYSTEMS{'gene'}. "-". $COORDINATE_SYSTEMS{'exon'};
my $intron_mapper =
$COORDINATE_SYSTEMS{'gene'}. "-". $COORDINATE_SYSTEMS{'intron'};
my $negative_intron_mapper =
$COORDINATE_SYSTEMS{'intron'}. "-". $COORDINATE_SYSTEMS{'negative_intron'};
my $exon_cds_mapper = $COORDINATE_SYSTEMS{'exon'}. "-". $COORDINATE_SYSTEMS{'cds'};
if(@value) {
if (ref($value[0]) &&
$value[0]->isa('Bio::SeqFeatureI') and
$value[0]->location->isa('Bio::Location::SplitLocationI')) {
@value = $value[0]->location->each_Location;
} else {
$self->throw("I need an array , not [@value]")
unless ref \@value eq 'ARRAY';
$self->throw("I need a reference to an array of Bio::LocationIs, not to [".
$value[0]. "]")
unless ref $value[0] and $value[0]->isa('Bio::LocationI');
}
#
# sort the input array
#
# and if the used has not defined CDS assume it is the complete exonic range
if (defined $value[0]->strand &&
$value[0]->strand == - 1) { #reverse strand
@value = map { $_->[0] }
sort { $b->[1] <=> $a->[1] }
map { [ $_, $_->start] }
@value;
unless ($self->cds) {
$self->cds(Bio::Location::Simple->new
(-start => $value[-1]->start,
-end => $value[0]->end,
-strand => $value[0]->strand,
-seq_id => $value[0]->seq_id,
-verbose => $self->verbose,
)
);
}
} else { # undef or forward strand
@value = map { $_->[0] }
sort { $a->[1] <=> $b->[1] }
map { [ $_, $_->start] }
@value;
unless ($self->cds) {
$self->cds(Bio::Location::Simple->new
(-start => $value[0]->start,
-end => $value[-1]->end,
-strand => $value[0]->strand,
-seq_id => $value[0]->seq_id,
-verbose => $self->verbose,
)
);
}
}
$self->{'_chr_exons'} = \@value;
# transform exons from chromosome to gene coordinates
# but only if gene coordinate system has been set
my @exons ;
#my $gene_mapper = $self->$COORDINATE_SYSTEMS{'chr'}. "-". $COORDINATE_SYSTEMS{'gene'};
my $gene_mapper = "1-2";
if (defined $self->{'_mappers'}->{$gene_mapper} ) {
my $tmp_in = $self->{'_in'};
my $tmp_out = $self->{'_out'};
my $tmp_verb = $self->verbose;
$self->verbose(0);
$self->in('chr');
$self->out('gene');
@exons = map {$self->map($_) } @value;
$self->{'_in'} = ($tmp_in);
$self->{'_out'} = ($tmp_out);
$self->verbose($tmp_verb);
} else {
@exons = @value;
}
my $cds_map = Bio::Coordinate::Collection->new;
my $inex_map = Bio::Coordinate::Collection->new;
my $exon_map = Bio::Coordinate::Collection->new;
my $exon_cds_map = Bio::Coordinate::Collection->new;
my $intron_map = Bio::Coordinate::Collection->new;
my $negative_intron_map = Bio::Coordinate::Collection->new;
my $tr_end = 0;
my $coffset;
my $exon_counter;
my $prev_exon_end;
for my $exon ( @exons ) {
$exon_counter++;
#
# gene -> cds
#
my $match1 = Bio::Location::Simple->new
(-seq_id =>'gene' ,
-start => $exon->start,
-end => $exon->end,
-strand => 1,
-verbose=> $self->verbose);
my $match2 = Bio::Location::Simple->new
(-seq_id => 'cds',
-start => $tr_end + 1,
-end => $tr_end + $exon->end - $exon->start +1,
-strand=>$exon->strand,
-verbose=>$self->verbose);
$cds_map->add_mapper(Bio::Coordinate::Pair->new
(-in => $match1,
-out => $match2,
)
);
if ($exon->start <= 1 and $exon->end >= 1) {
$coffset = $tr_end - $exon->start + 1;
}
$tr_end = $tr_end + $exon->end - $exon->start + 1;
#
# gene -> intron
#
if (defined $prev_exon_end) {
my $match3 = Bio::Location::Simple->new
(-seq_id => 'gene',
-start => $prev_exon_end + 1,
-end => $exon->start -1,
-strand => $exon->strand,
-verbose => $self->verbose);
my $match4 = Bio::Location::Simple->new
(-seq_id => 'intron'. ($exon_counter -1),
-start => 1,
-end => $exon->start - 1 - $prev_exon_end,
-strand =>$exon->strand,
-verbose => $self->verbose,);
# negative intron coordinates
my $match5 = Bio::Location::Simple->new
(-seq_id => 'intron'. ($exon_counter -1),
-start => -1 * ($exon->start - 2 - $prev_exon_end) -1,
-end => -1,
-strand => $exon->strand,
-verbose => $self->verbose);
$inex_map->add_mapper(Bio::Coordinate::Pair->new
(-in => $match3,
-out => $match4
)
);
$intron_map->add_mapper(Bio::Coordinate::Pair->new
(-in => $self->_clone_loc($match3),
-out => $self->_clone_loc($match4)
)
);
$negative_intron_map->add_mapper(Bio::Coordinate::Pair->new
(-in => $self->_clone_loc($match4),
-out => $match5
));
}
# store the value
$prev_exon_end = $exon->end;
#
# gene -> exon
#
my $match6 = Bio::Location::Simple->new
(-seq_id => 'exon'. $exon_counter,
-start => 1,
-end => $exon->end - $exon->start +1,
-strand => $exon->strand,
-verbose=> $self->verbose,);
my $pair2 = Bio::Coordinate::Pair->new(-in => $self->_clone_loc($match1),
-out => $match6
);
my $pair3 = Bio::Coordinate::Pair->new(-in => $self->_clone_loc($match6),
-out => $self->_clone_loc($match2)
);
$inex_map->add_mapper(Bio::Coordinate::Pair->new
(-in => $self->_clone_loc($match1),
-out => $match6
)
);
$exon_map->add_mapper(Bio::Coordinate::Pair->new
(-in => $self->_clone_loc($match1),
-out => $self->_clone_loc($match6)
)
);
$exon_cds_map->add_mapper(Bio::Coordinate::Pair->new
(-in => $self->_clone_loc($match6),
-out => $self->_clone_loc($match2)
)
);
}
# move coordinate start if exons have negative values
if ($coffset) {
foreach my $m ($cds_map->each_mapper) {
$m->out->start($m->out->start - $coffset);
$m->out->end($m->out->end - $coffset);
}
}
$self->{'_mappers'}->{$cds_mapper} = $cds_map;
$self->{'_mappers'}->{$exon_cds_mapper} = $exon_cds_map;
$self->{'_mappers'}->{$inex_mapper} = $inex_map;
$self->{'_mappers'}->{$exon_mapper} = $exon_map;
$self->{'_mappers'}->{$intron_mapper} = $intron_map;
$self->{'_mappers'}->{$negative_intron_mapper} = $negative_intron_map;
}
return @{$self->{'_chr_exons'}} || 0;
}
=head2 _clone_loc
Title : _clone_loc
Usage : $copy_of_loc = $obj->_clone_loc($loc);
Function: Make a deep copy of a simple location
Returns : a Bio::Location::Simple object
Args : a Bio::Location::Simple object to be cloned
=cut
sub _clone_loc { # clone a simple location
my ($self,$loc) = @_;
$self->throw("I need a Bio::Location::Simple , not [". ref $loc. "]")
unless $loc->isa('Bio::Location::Simple');
return Bio::Location::Simple->new
(-verbose => $self->verbose,
-seq_id => $loc->seq_id,
-start => $loc->start,
-end => $loc->end,
-strand => $loc->strand,
-location_type => $loc->location_type
);
}
=head2 cds
Title : cds
Usage : $obj->cds(20);
Function: Set and read the offset of CDS from the start of transcipt
Simple input can be an integer which gives the start of the
coding region in genomic coordinate. If you want to provide
the end of the coding region or indicate the use of the
opposite strand, you have to pass a Bio::RangeI
(e.g. Bio::Location::Simple or Bio::SegFeature::Generic)
object to this method.
Returns : set value or 0
Args : new value (optional)
=cut
sub cds {
my ($self,$value) = @_;
if( defined $value) {
if ($value =~ /^[+-]?\d+$/ ) {
my $loc = Bio::Location::Simple->new(-start=>$value, -end => $value,
-verbose=>$self->verbose);
$self->{'_cds'} = $loc;
}
elsif (ref $value && $value->isa('Bio::RangeI') ) {
$self->{'_cds'} = $value;
} else {
$self->throw("I need an integer or Bio::RangeI, not [$value]")
}
# strand !!
my $len;
$len = $self->{'_cds'}->end - $self->{'_cds'}->start +1
if defined $self->{'_cds'}->end;
my $a = $self->_create_pair
('chr', 'gene', 0,
$self->{'_cds'}->start-1,
$len,
$self->{'_cds'}->strand);
my $mapper = $COORDINATE_SYSTEMS{'chr'}. "-". $COORDINATE_SYSTEMS{'gene'};
$self->{'_mappers'}->{$mapper} = $a;
# recalculate exon-based mappers
if ( defined $self->{'_chr_exons'} ) {
$self->exons(@{$self->{'_chr_exons'}});
}
}
return $self->{'_cds'} || 0;
}
=head2 map
Title : map
Usage : $newpos = $obj->map(5);
Function: Map the location from the input coordinate system
to a new value in the output coordinate system.
Example :
Returns : new value in the output coordiante system
Args : a Bio::Location::Simple
=cut
sub map {
my ($self,$value) = @_;
my ($res);
$self->throw("Need to pass me a Bio::Location::Simple or ".
"Bio::Location::Simple or Bio::SeqFeatureI, not [".
ref($value). "]")
unless ref($value) && ($value->isa('Bio::Location::Simple') or
$value->isa('Bio::Location::SplitLocationI') or
$value->isa('Bio::SeqFeatureI'));
$self->throw("Input coordinate system not set")
unless $self->{'_in'};
$self->throw("Output coordinate system not set")
unless $self->{'_out'};
$self->throw("Do not be silly. Input and output coordinate ".
"systems are the same!")
unless $self->{'_in'} != $self->{'_out'};
$self->_check_direction();
$value = $value->location if $value->isa('Bio::SeqFeatureI');
$self->debug( "=== Start location: ". $value->start. ",".
$value->end. " (". ($value->strand || ''). ")\n");
# if nozero coordinate system is used in the input values
if ( defined $self->{'_nozero'} &&
( $self->{'_nozero'} == 1 || $self->{'_nozero'} == 3 ) ) {
$value->start($value->start + 1)
if defined $value->start && $value->start < 1;
$value->end($value->end + 1)
if defined $value->end && $value->end < 1;
}
my @steps = $self->_get_path();
$self->debug( "mapping ". $self->{'_in'}. "->". $self->{'_out'}.
" Mappers: ". join(", ", @steps). "\n");
foreach my $mapper (@steps) {
if ($mapper eq $TRANSLATION) {
if ($self->direction == 1) {
$value = $self->_translate($value);
$self->debug( "+ $TRANSLATION cds -> propeptide (translate) \n");
} else {
$value = $self->_reverse_translate($value);
$self->debug("+ $TRANSLATION propeptide -> cds (reverse translate) \n");
}
}
# keep the start and end values, and go on to next iteration
# if this mapper is not set
elsif ( ! defined $self->{'_mappers'}->{$mapper} ) {
# update mapper name
$mapper =~ /\d+-(\d+)/; my ($counter) = $1;
$value->seq_id($COORDINATE_INTS{$counter});
$self->debug( "- $mapper\n");
} else {
#
# the DEFAULT : generic mapping
#
$value = $self->{'_mappers'}->{$mapper}->map($value);
$value->purge_gaps
if ($value && $value->isa('Bio::Location::SplitLocationI') &&
$value->can('gap'));
$self->debug( "+ $mapper (". $self->direction. "): start ".
$value->start. " end ". $value->end. "\n")
if $value && $self->verbose > 0;
}
}
# if nozero coordinate system is asked to be used in the output values
if ( defined $value && defined $self->{'_nozero'} &&
( $self->{'_nozero'} == 2 || $self->{'_nozero'} == 3 ) ) {
$value->start($value->start - 1)
if defined $value->start && $value->start < 1;
$value->end($value->end - 1)
if defined $value->end && $value->end < 1;
}
# handle merging of adjacent split locations!
if (ref $value eq "Bio::Coordinate::Result" && $value->each_match > 1 ) {
my $prevloc;
my $merging = 0;
my $newvalue;
my @matches;
foreach my $loc ( $value->each_Location(1) ) {
unless ($prevloc) {
$prevloc = $loc;
push @matches, $prevloc;
next;
}
if ($prevloc->end == ($loc->start - 1) &&
$prevloc->seq_id eq $loc->seq_id) {
$prevloc->end($loc->end);
$merging = 1;
} else {
push @matches, $loc;
$prevloc = $loc;
}
}
if ($merging) {
if (@matches > 1 ) {
$newvalue = Bio::Coordinate::Result->new;
map {$newvalue->add_sub_Location} @matches;
} else {
$newvalue = Bio::Coordinate::Result::Match->new
(-seq_id => $matches[0]->seq_id,
-start => $matches[0]->start,
-end => $matches[0]->end,
-strand => $matches[0]->strand,
-verbose => $self->verbose,);
}
$value = $newvalue;
}
}
elsif (ref $value eq "Bio::Coordinate::Result" &&
$value->each_match == 1 ){
$value = $value->match;
}
return $value;
}
=head2 direction
Title : direction
Usage : $obj->direction('peptide');
Function: Read-only method for the direction of mapping deduced from
predefined input and output coordinate names.
Example :
Returns : 1 or -1, mapping direction
Args : new value (optional)
=cut
sub direction {
my ($self) = @_;
return $self->{'_direction'};
}
=head2 swap
Title : swap
Usage : $obj->swap;
Function: Swap the direction of transformation
(input <-> output)
Example :
Returns : 1
Args :
=cut
sub swap {
my ($self,$value) = @_;
($self->{'_in'}, $self->{'_out'}) = ($self->{'_out'}, $self->{'_in'});
map { $self->{'_mappers'}->{$_}->swap } keys %{$self->{'_mappers'}};
# record the changed direction;
$self->{_direction} *= -1;
return 1;
}
=head2 to_string
Title : to_string
Usage : $newpos = $obj->to_string(5);
Function: Dump the internal mapper values into a human readable format
Example :
Returns : string
Args :
=cut
sub to_string {
my ($self) = shift;
print "-" x 40, "\n";
# chr-gene
my $mapper_str = 'chr-gene';
my $mapper = $self->_mapper_string2code($mapper_str);
printf "\n %-12s (%s)\n", $mapper_str, $mapper ;
if (defined $self->cds) {
my $end = $self->cds->end -1 if defined $self->cds->end;
printf "%16s%s: %s (%s)\n", ' ', 'gene offset', $self->cds->start-1 , $end || '';
printf "%16s%s: %s\n", ' ', 'gene strand', $self->cds->strand || 0;
}
# gene-intron
$mapper_str = 'gene-intron';
$mapper = $self->_mapper_string2code($mapper_str);
printf "\n %-12s (%s)\n", $mapper_str, $mapper ;
my $i = 1;
foreach my $pair ( $self->{'_mappers'}->{$mapper}->each_mapper ) {
printf "%8s :%8s -> %-12s\n", $i, $pair->in->start, $pair->out->start ;
printf "%8s :%8s -> %-12s\n", '', $pair->in->end, $pair->out->end ;
$i++;
}
# intron-negative_intron
$mapper_str = 'intron-negative_intron';
$mapper = $self->_mapper_string2code($mapper_str);
printf "\n %-12s (%s)\n", $mapper_str, $mapper ;
$i = 1;
foreach my $pair ( $self->{'_mappers'}->{$mapper}->each_mapper ) {
printf "%8s :%8s -> %-12s\n", $i, $pair->in->start, $pair->out->start ;
printf "%8s :%8s -> %-12s\n", '', $pair->in->end, $pair->out->end ;
$i++;
}
# gene-exon
$mapper_str = 'gene-exon';
$mapper = $self->_mapper_string2code($mapper_str);
printf "\n %-12s (%s)\n", $mapper_str, $mapper ;
$i = 1;
foreach my $pair ( $self->{'_mappers'}->{$mapper}->each_mapper ) {
printf "%8s :%8s -> %-12s\n", $i, $pair->in->start, $pair->out->start ;
printf "%8s :%8s -> %-12s\n", '', $pair->in->end, $pair->out->end ;
$i++;
}
# gene-cds
$mapper_str = 'gene-cds';
$mapper = $self->_mapper_string2code($mapper_str);
printf "\n %-12s (%s)\n", $mapper_str, $mapper ;
$i = 1;
foreach my $pair ( $self->{'_mappers'}->{$mapper}->each_mapper ) {
printf "%8s :%8s -> %-12s\n", $i, $pair->in->start, $pair->out->start ;
printf "%8s :%8s -> %-12s\n", '', $pair->in->end, $pair->out->end ;
$i++;
}
# cds-propeptide
$mapper_str = 'cds-propeptide';
$mapper = $self->_mapper_string2code($mapper_str);
printf "\n %-12s (%s)\n", $mapper_str, $mapper ;
printf "%9s%-12s\n", "", '"translate"';
# propeptide-peptide
$mapper_str = 'propeptide-peptide';
$mapper = $self->_mapper_string2code($mapper_str);
printf "\n %-12s (%s)\n", $mapper_str, $mapper ;
printf "%16s%s: %s\n", ' ', "peptide offset", $self->peptide_offset;
print "\nin : ", $self->in, "\n";
print "out: ", $self->out, "\n";
my $dir;
$self->direction ? ($dir='forward') : ($dir='reverse');
printf "direction: %-8s(%s)\n", $dir, $self->direction;
print "\n", "-" x 40, "\n";
1;
}
sub _mapper_code2string {
my ($self, $code) = @_;
my ($a, $b) = $code =~ /(\d+)-(\d+)/;
return $COORDINATE_INTS{$a}. '-'. $COORDINATE_INTS{$b};
}
sub _mapper_string2code {
my ($self, $string) =@_;
my ($a, $b) = $string =~ /([^-]+)-(.*)/;
return $COORDINATE_SYSTEMS{$a}. '-'. $COORDINATE_SYSTEMS{$b};
}
=head2 _create_pair
Title : _create_pair
Usage : $mapper = $obj->_create_pair('chr', 'gene', 0, 2555, 10000, -1);
Function: Internal helper method to create a mapper between
two coordinate systems
Returns : a Bio::Coordinate::Pair object
Args : string, input coordinate system name,
string, output coordinate system name,
boolean, strict mapping
positive integer, offset
positive integer, length
1 || -1 , strand
=cut
sub _create_pair {
my ($self, $in, $out, $strict, $offset, $length, $strand ) = @_;
$strict ||= 0;
$strand ||= 1;
$length ||= 20;
my $match1 = Bio::Location::Simple->new
(-seq_id => $in,
-start => $offset+1,
-end => $offset+$length,
-strand => 1,
-verbose => $self->verbose);
my $match2 = Bio::Location::Simple->new
(-seq_id => $out,
-start => 1,
-end => $length,
-strand => $strand,
-verbose => $self->verbose);
my $pair = Bio::Coordinate::ExtrapolatingPair->new
(-in => $match1,
-out => $match2,
-strict => $strict,
-verbose => $self->verbose,
);
return $pair;
}
=head2 _translate
Title : _translate
Usage : $newpos = $obj->_translate($loc);
Function: Translate the location from the CDS coordinate system
to a new value in the propeptide coordinate system.
Example :
Returns : new location
Args : a Bio::Location::Simple or Bio::Location::SplitLocationI
=cut
sub _translate {
my ($self,$value) = @_;
$self->throw("Need to pass me a Bio::Location::Simple or ".
"Bio::Location::SplitLocationI, not [". ref($value). "]")
unless defined $value &&
($value->isa('Bio::Location::Simple') || $value->isa('Bio::Location::SplitLocationI'));
my $seqid = 'propeptide';
if ($value->isa("Bio::Location::SplitLocationI") ) {
my $split = Bio::Location::Split->new(-seq_id=>$seqid);
foreach my $loc ( $value->each_Location(1) ) {
my $match = Bio::Location::Simple->new
(-start => int ($loc->start / 3 ) +1,
-end => int ($loc->end / 3 ) +1,
-seq_id => $seqid,
-strand => 1,
-verbose => $self->verbose,
);
$split->add_sub_Location($match);
}
return $split;
} else {
return new Bio::Location::Simple(-start => int($value->start / 3 )+1,
-end => int($value->end / 3 )+1,
-seq_id => $seqid,
-strand => 1,
-verbose=> $self->verbose,
);
}
}
sub _frame {
my ($self,$value) = @_;
$self->throw("Need to pass me a Bio::Location::Simple or ".
"Bio::Location::SplitLocationI, not [". ref($value). "]")
unless defined $value &&
($value->isa('Bio::Location::Simple') || $value->isa('Bio::Location::SplitLocationI'));
my $seqid = 'propeptide';
if ($value->isa("Bio::Location::SplitLocationI")) {
my $split = Bio::Location::Split->new(-seq_id=>$seqid);
foreach my $loc ( $value->each_Location(1) ) {
my $match = Bio::Location::Simple->new
(-start => ($value->start-1) % 3 +1,
-end => ($value->end-1) % 3 +1,
-seq_id => 'frame',
-strand => 1,
-verbose=> $self->verbose);
$split->add_sub_Location($match);
}
return $split;
} else {
return new Bio::Location::Simple(-start => ($value->start-1) % 3 +1,
-end => ($value->end-1) % 3 +1,
-seq_id => 'frame',
-strand => 1,
-verbose => $self->verbose,
);
}
}
=head2 _reverse_translate
Title : _reverse_translate
Usage : $newpos = $obj->_reverse_translate(5);
Function: Reverse translate the location from the propeptide
coordinate system to a new value in the CSD.
Note that a single peptide location expands to cover
the codon triplet
Example :
Returns : new location in the CDS coordinate system
Args : a Bio::Location::Simple or Bio::Location::SplitLocationI
=cut
sub _reverse_translate {
my ($self,$value) = @_;
$self->throw("Need to pass me a Bio::Location::Simple or ".
"Bio::Location::SplitLocationI, not [". ref($value). "]")
unless defined $value &&
($value->isa('Bio::Location::Simple') || $value->isa('Bio::Location::SplitLocationI'));
my $seqid = 'cds';
if ($value->isa("Bio::Location::SplitLocationI")) {
my $split = Bio::Location::Split->new(-seq_id=>$seqid);
foreach my $loc ( $value->each_Location(1) ) {
my $match = Bio::Location::Simple->new
(-start => $value->start * 3 - 2,
-end => $value->end * 3,
-seq_id => $seqid,
-strand => 1,
-verbose => $self->verbose,
);
$split->add_sub_Location($match);
}
return $split;
} else {
return new Bio::Location::Simple(-start => $value->start * 3 - 2,
-end => $value->end * 3,
-seq_id => $seqid,
-strand => 1,
-verbose => $self->verbose,
);
}
}
=head2 _check_direction
Title : _check_direction
Usage : $obj->_check_direction();
Function: Check and swap when needed the direction the location
mapping Pairs based on input and output values
Example :
Returns : new location
Args : a Bio::Location::Simple
=cut
sub _check_direction {
my ($self) = @_;
my $new_direction = 1;
$new_direction = -1 if $self->{'_in'} > $self->{'_out'};
unless ($new_direction == $self->{_direction} ) {
map { $self->{'_mappers'}->{$_}->swap } keys %{$self->{'_mappers'}};
# record the changed direction;
$self->{_direction} *= -1;
}
1;
}
=head2 _get_path
Title : _get_path
Usage : $obj->_get_path('peptide');
Function: internal method for finding that shortest path between
input and output coordinate systems.
Calculations and caching are handled by the graph class.
See L<Bio::Coordinate::Graph>.
Example :
Returns : array of the mappers
Args : none
=cut
sub _get_path {
my ($self) = @_;
my $start = $self->{'_in'} || 0;
my $end = $self->{'_out'} || 0;
# note the order
# always go from smaller to bigger: it makes caching more efficient
my $reverse;
if ($start > $end) {
($start, $end) = ($end, $start );
$reverse++;
}
my @mappers;
if (exists $self->{'_previous_path'} and
$self->{'_previous_path'} eq "$start$end" ) {
# use cache
@mappers = @{$self->{'_mapper_path'}};
} else {
my $mapper;
my $prev_node = '';
@mappers =
map { $mapper = "$prev_node-$_"; $prev_node = $_; $mapper; }
$self->{'_graph'}->shortest_path($start, $end);
shift @mappers;
$self->{'_previous_path'} = "$start$end";
$self->{'_mapper_path'} = \@mappers;
}
$reverse ? return reverse @mappers : return @mappers;
}
1;