#
# BioPerl module for Bio::Assembly::Scaffold
#
# Copyright by Robson F. de Souza
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Assembly::Scaffold - Perl module to hold and manipulate sequence assembly
data.
=head1 SYNOPSIS
#
# Module loading
use Bio::Assembly::IO;
# Assembly loading methods
my $aio = Bio::Assembly::IO->new(-file=>"test.ace.1", -format=>'phrap');
my $assembly = $aio->next_assembly;
foreach my $contig ($assembly->all_contigs) {
# do something... (see Bio::Assembly::Contig)
}
=head1 DESCRIPTION
Bio::Assembly::Scaffold was developed to store and manipulate data
from sequence assembly programs like Phrap. It implements the
ScaffoldI interface and intends to be generic enough to be used by
Bio::Assembly::IO drivers written to programs other than Phrap.
=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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Robson Francisco de Souza
rfsouza@citri.iq.usp.br
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Assembly::Scaffold;
use strict;
use Bio::Annotation::Collection;
use base qw(Bio::Root::Root Bio::Assembly::ScaffoldI);
=head2 new ()
Title : new
Usage : $scaffold = new ( -id => "assembly 1",
-source => 'program_name',
-contigs => \@contigs,
-singlets => \@singlets );
Function: creates a new scaffold object
Returns : Bio::Assembly::Scaffold
Args : -id : [string] scaffold name
-source : [string] sequence assembly program
-contigs : reference to array of Bio::Assembly::Contig objects
-singlets : reference to array of Bio::Assembly::Singlet objects
=cut
sub new {
my($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($id, $src, $contigs, $singlets) = $self->_rearrange(
[qw(ID SOURCE CONTIGS SINGLETS)], @args);
# Scaffold defaults
$self->{'_id'} = 'NoName';
$self->{'_source'} = 'Unknown';
$self->{'_contigs'} = {};
$self->{'_singlets'} = {};
$self->{'_seqs'} = {};
$self->{'_annotation'} = Bio::Annotation::Collection->new();
# Import manual info
$self->{'_id'} = $id if (defined $id);
$self->{'_source'} = $src if (defined $src);
# Add contigs and singlets to scaffold
if (defined $contigs && ref($contigs = 'ARRAY')) {
for my $contig (@{$contigs}) {
if( ! ref $contig || ! $contig->isa('Bio::Assembly::Contig') ) {
$self->throw("Bio::Assembly::Scaffold::new is unable to process non".
"Bio::Assembly::Contig object [", ref($contig), "]");
}
$self->add_contig($contig);
}
}
if (defined $singlets && ref($singlets = 'ARRAY')) {
for my $singlet (@{$singlets}) {
if( ! ref $singlet || ! $singlet->isa('Bio::Assembly::Singlet') ) {
$self->throw("Bio::Assembly::Scaffold::new is unable to process non".
"Bio::Assembly::Singlet object [", ref($singlet), "]");
}
$self->add_singlet($singlet);
}
}
return $self;
}
=head1 Accessing general assembly data
=cut
=head2 id
Title : id
Usage : $assembly->id()
Function: Get/Set assembly ID
Returns : string or undef
Args : string
=cut
sub id {
my ($self, $id) = @_;
return $self->{'_id'} = $id if (defined $id);
return $self->{'_id'};
}
=head2 annotation
Title : annotation
Usage : $assembly->annotation()
Function: Get/Set assembly annotation object
Returns : Bio::Annotation::Collection
Args : none
=cut
sub annotation {
my ($self, $ref) = shift;
$self->{'_annotation'} = $ref if (defined $ref);
return $self->{'_annotation'};
}
=head2 get_nof_contigs
Title : get_nof_contigs
Usage : $assembly->get_nof_contigs()
Function: Get the number of contigs included in the scaffold
Returns : integer
Args : none
=cut
sub get_nof_contigs {
my $self = shift;
return scalar( $self->get_contig_ids() );
}
=head2 get_nof_contig_seqs
Title : get_nof_contig_seqs
Usage : $assembly->get_nof_contig_seqs()
Function: Get the number of sequences included in contigs of the
scaffold (no consensus sequences or singlets)
Returns : integer
Args : none
=cut
sub get_nof_contig_seqs {
my $self = shift;
my $nof_seqs = 0;
foreach my $contig ($self->all_contigs) {
$nof_seqs += scalar( $contig->get_seq_ids() );
}
return $nof_seqs;
}
# function alias for backward compatibility
*get_nof_sequences_in_contigs = \&get_nof_contig_seqs;
=head2 get_nof_singlets (get_nof_singlet_seqs)
Title : nof_singlets
Usage : $assembly->nof_singlets()
Function: Get the number of singlets included in the assembly
Returns : integer
Args : none
=cut
sub get_nof_singlets {
my $self = shift;
return scalar( $self->get_singlet_ids() );
}
*get_nof_singlet_seqs = \&get_nof_singlets;
=head2 get_all_seq_ids
Title : get_all_seq_ids
Usage : $assembly->get_all_seq_ids()
Function: Get the ID of all sequences making up the scaffold
(sequences from contigs and singlets, not consensus).
Returns : array of strings
Args : none
=cut
sub get_all_seq_ids {
my $self = shift;
return keys %{ $self->{'_seqs'} };
}
=head2 get_nof_seqs
Title : get_nof_seqs
Usage : $assembly->get_nof_seqs()
Function: Get total number of sequences making up the scaffold
(sequences from contigs and singlets, not consensus).
Returns : integer
Args : none
=cut
sub get_nof_seqs {
my $self = shift;
return scalar $self->get_all_seq_ids;
}
=head2 get_contig_seq_ids
Title : get_contig_seq_ids
Usage : $assembly->get_contig_seq_ids()
Function: Get the ID of all sequences in contigs
Returns : array of strings
Args : none
=cut
sub get_contig_seq_ids {
my $self = shift;
my @ids;
for my $contig ( $self->all_contigs ) {
push @ids, $contig->get_seq_ids;
}
return @ids;
}
# function alias for backward compatibility
*get_seq_ids = \&get_contig_seq_ids;
=head2 get_contig_ids
Title : get_contig_ids
Usage : $assembly->get_contig_ids()
Function: Access list of contig IDs from assembly
Returns : an array, if there are any contigs in the
assembly. An empty array otherwise
Args : none
=cut
sub get_contig_ids {
my $self = shift;
return wantarray
? sort keys %{$self->{'_contigs'}}
: scalar keys %{$self->{'_contigs'}};
}
=head2 get_singlet_ids (get_singlet_seq_ids)
Title : get_singlet_ids
Usage : $assembly->get_singlet_ids()
Function: Access list of singlet IDs from assembly
Returns : array of strings if there are any singlets
otherwise an empty array
Args : none
=cut
sub get_singlet_ids {
my $self = shift;
return wantarray
? sort keys %{$self->{'_singlets'}}
: scalar keys %{$self->{'_singlets'}};
}
*get_singlet_seq_ids = \&get_singlet_ids;
=head2 get_seq_by_id
Title : get_seq_by_id
Usage : $assembly->get_seq_by_id($id)
Function: Get a reference for an sequence making up the scaffold
(from a contig or singlet, not consensus)
Returns : a Bio::LocatableSeq object
undef if sequence $id is not found in the scaffold
Args : [string] sequence identifier (id)
=cut
sub get_seq_by_id {
my $self = shift;
my $seqID = shift;
return unless (exists $self->{'_seqs'}{$seqID});
return $self->{'_seqs'}{$seqID}->get_seq_by_name($seqID);
}
=head2 get_contig_by_id
Title : get_contig_by_id
Usage : $assembly->get_contig_by_id($id)
Function: Get a reference for a contig
Returns : a Bio::Assembly::Contig object or undef
Args : [string] contig unique identifier (ID)
=cut
sub get_contig_by_id {
my $self = shift;
my $contigID = shift;
return unless (exists $self->{'_contigs'}{$contigID});
return $self->{'_contigs'}{$contigID};
}
=head2 get_singlet_by_id
Title : get_singlet_by_id
Usage : $assembly->get_singlet_by_id()
Function: Get a reference for a singlet
Returns : Bio::Assembly::Singlet object or undef
Args : [string] a singlet ID
=cut
sub get_singlet_by_id {
my $self = shift;
my $singletID = shift;
return unless (exists $self->{'_singlets'}{$singletID});
return $self->{'_singlets'}{$singletID};
}
=head1 Modifier methods
=cut
=head2 add_contig
Title : add_contig
Usage : $assembly->add_contig($contig)
Function: Add a contig to the assembly
Returns : 1 on success
Args : a Bio::Assembly::Contig object
order (optional)
=cut
sub add_contig {
my ($self, $contig) = @_;
# Input check
if( !ref $contig || ! $contig->isa('Bio::Assembly::Contig') ) {
$self->throw("Bio::Assembly::Scaffold::add_contig is unable to process".
" non Bio::Assembly::Contig object [", ref($contig), "]");
}
# Create and attribute contig ID
my $contigID = $contig->id();
if( !defined $contigID ) {
$contigID = 'Unknown_' . ($self->get_nof_contigs() + 1);
$contig->id($contigID);
$self->warn("Attributing ID $contigID to unnamed Bio::Assembly::Contig".
" object.");
}
# Adding contig to scaffold
$self->warn("Replacing contig $contigID with a new contig object")
if (exists $self->{'_contigs'}{$contigID});
$self->{'_contigs'}{$contigID} = $contig;
$contig->assembly($self); # weak circular reference
# Put contig sequences in the list of sequences belonging to the scaffold
foreach my $seqID ($contig->get_seq_ids()) {
if (exists $self->{'_seqs'}{$seqID} &&
not($self->{'_seqs'}{$seqID} eq $contig) ) {
$self->warn( "Sequence $seqID already assigned to object ".
$self->{'_seqs'}{$seqID}->id().". Moving to contig $contigID");
}
$self->{'_seqs'}{$seqID} = $contig;
}
return 1;
}
=head2 add_singlet
Title : add_singlet
Usage : $assembly->add_singlet($seq)
Function: Add a singlet to the assembly
Returns : 1 on success
Args : a Bio::Assembly::Singlet object
order (optional)
=cut
sub add_singlet {
my ($self, $singlet) = @_;
# Input check
if ( !ref $singlet || ! $singlet->isa('Bio::Assembly::Singlet') ) {
$self->throw("Bio::Assembly::Scaffold::add_singlet is unable to process".
" non Bio::Assembly::Singlet object [", ref($singlet), "]");
}
# Create and attribute singlet ID
my $singletID = $singlet->id();
if( !defined $singletID ) {
$singletID = 'Unknown_' . ($self->get_nof_singlets() + 1);
$singlet->id($singletID);
$self->warn("Attributing ID $singletID to unnamed Bio::Assembly::".
"Singlet object.");
}
# Adding singlet to scaffold
$self->warn("Replacing singlet $singletID with a new singlet object")
if (exists $self->{'_singlets'}{$singletID});
$self->{'_singlets'}{$singletID} = $singlet;
$singlet->assembly($self); # weak circular reference
# Put singlet sequence in the list of sequences belonging to the scaffold
my $seqID = $singlet->seqref->id();
if (exists $self->{'_seqs'}{$seqID} &&
not($self->{'_seqs'}{$seqID} eq $singlet) ) {
$self->warn( "Sequence $seqID already assigned to object ".
$self->{'_seqs'}{$seqID}->id().". Moving to singlet $singletID");
}
$self->{'_seqs'}{$seqID} = $singlet;
return 1;
}
=head2 update_seq_list
Title : update_seq_list
Usage : $assembly->update_seq_list()
Function:
Synchronizes the assembly registry for sequences in
contigs and contig actual aligned sequences content. You
probably want to run this after you remove/add a
sequence from/to a contig in the assembly.
Returns : 1 for success
Args : none
=cut
sub update_seq_list {
my $self = shift;
$self->{'_seqs'} = {};
# Put sequences in contigs in list of sequences belonging to the scaffold
foreach my $contig ($self->all_contigs) {
my $contigID = $contig->id();
foreach my $seqID ($contig->get_seq_ids) {
if (exists $self->{'_seqs'}{$seqID} &&
not($self->{'_seqs'}{$seqID} eq $contig) ) {
$self->warn( "Sequence $seqID already assigned to object ".
$self->{'_seqs'}{$seqID}->id().". Moving to contig $contigID");
}
$self->{'_seqs'}{$seqID} = $contig;
}
}
# Put singlet sequences in the list of sequences belonging to the scaffold
foreach my $singlet ($self->all_singlets) {
my $singletID = $singlet->id();
my $seqID = $singlet->seqref->id();
if (exists $self->{'_seqs'}{$seqID} &&
not($self->{'_seqs'}{$seqID} eq $singlet) ) {
$self->warn( "Sequence $seqID already assigned to object ".
$self->{'_seqs'}{$seqID}->id().". Moving to singlet $singletID");
}
$self->{'_seqs'}{$seqID} = $singlet;
}
return 1;
}
=head2 remove_contigs
Title : remove_contigs
Usage : $assembly->remove_contigs(1..4)
Function: Remove contig from assembly object
Returns : an array of removed Bio::Assembly::Contig
objects
Args : an array of contig IDs
See function get_contig_ids() above
=cut
sub remove_contigs {
my ($self, @args) = @_;
my @ret = ();
foreach my $contigID (@args) {
foreach my $seqID ($self->get_contig_by_id($contigID)->get_seq_ids()) {
delete $self->{'_seqs'}{$seqID};
}
push(@ret, $self->{'_contigs'}{$contigID});
delete $self->{'_contigs'}{$contigID};
}
return @ret;
}
=head2 remove_singlets
Title : remove_singlets
Usage : $assembly->remove_singlets(@singlet_ids)
Function: Remove singlet from assembly object
Returns : the Bio::Assembly::Singlet objects removed
Args : a list of singlet IDs
See function get_singlet_ids() above
=cut
sub remove_singlets {
my ($self,@args) = @_;
my @ret = ();
foreach my $singletID (@args) {
push(@ret,$self->{'_singlets'}{$singletID});
delete $self->{'_singlets'}{$singletID};
}
return @ret;
}
=head2 remove_features_collection
Title : remove_features_collection
Usage : $assembly->remove_features_collection()
Function: Removes the collection of features associated to every
contig and singlet of the scaffold. This can be useful
to save some memory (when contig and singlet features are
not needed).
Returns : none
Argument : none
=cut
sub remove_features_collection {
my ($self) = @_;
for my $obj ( $self->all_contigs, $self->all_singlets ) {
$obj->remove_features_collection;
}
return;
}
=head1 Contig and singlet selection methods
=cut
=head2 select_contigs
Title : select_contigs
Usage : $assembly->select_contigs(@list)
Function: Select an array of contigs from the assembly
Returns : an array of Bio::Assembly::Contig objects
Args : an array of contig ids
See function get_contig_ids() above
=cut
sub select_contigs {
my ($self,@args) = @_;
my @contigs = ();
foreach my $contig (@args) {
unless (exists $self->{'_contigs'}{$contig}) {
$self->warn("$contig contig not found. Ignoring...");
next;
}
push(@contigs, $self->{'_contigs'}{$contig});
}
return @contigs;
}
=head2 select_singlets
Title : select_singlets
Usage : $assembly->select_singlets(@list)
Function: Selects an array of singlets from the assembly
Returns : an array of Bio::Assembly::Singlet objects
Args : an array of singlet ids
See function get_singlet_ids() above
=cut
sub select_singlets {
my ($self,@args) = @_;
my @singlets = ();
foreach my $singlet (@args) {
unless (exists $self->{'_singlets'}{$singlet}) {
$self->warn("$singlet singlet not found. Ignoring...");
next;
}
push(@singlets, $self->{'_singlets'}{$singlet});
}
return @singlets;
}
=head2 all_contigs
Title : all_contigs
Usage : my @contigs = $assembly->all_contigs
Function:
Returns a list of all contigs in this assembly. Contigs
are both clusters and alignments of one or more reads,
with an associated consensus sequence.
Returns : array of Bio::Assembly::Contig (in lexical id order)
Args : none
=cut
sub all_contigs {
my ($self) = @_;
my @contigs = ();
foreach my $contig (sort { $a cmp $b } keys %{ $self->{'_contigs'} }) {
push(@contigs, $self->{'_contigs'}{$contig});
}
return @contigs;
}
=head2 all_singlets
Title : all_singlets
Usage : my @singlets = $assembly->all_singlets
Function:
Returns a list of all singlets in this assembly.
Singlets are isolated reads, without non-vector
matches to any other read in the assembly.
Returns : array of Bio::Assembly::Singlet objects (in lexical order by id)
Args : none
=cut
sub all_singlets {
my ($self) = @_;
my @singlets = ();
foreach my $singlet (sort { $a cmp $b } keys %{ $self->{'_singlets'} }) {
push(@singlets, $self->{'_singlets'}{$singlet});
}
return @singlets;
}
1;