Raw content of Bio::Assembly::Scaffold
<![CDATA[# $Id: Scaffold.pm,v 1.2 2002/11/11 18:16:30 lapp Exp $
#
# 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 SYNOPSYS
# Module loading
use Bio::Assembly::IO;
# Assembly loading methods
my $aio = new Bio::Assembly::IO(-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://bio.perl.org/MailList.html - About the mailing lists
=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 email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=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 vars qw(@ISA $VERSION);
use Bio::Root::Root;
use Bio::Assembly::ScaffoldI;
use Bio::Annotation::Collection;
$VERSION = '0.0.1';
@ISA = qw(Bio::Root::Root Bio::Assembly::ScaffoldI);
=head2 new ()
Title : new
Usage : $assembly = new (-source=>'program_name',
-contigs=>\@contigs,
-id=>"assembly 1");
Function: creates a new assembly object
Returns :
Args :
-source : [string] sequence assembly program
-contigs : reference to array of
Bio::Assembly::Contig objects
-id : [string] assembly name
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($src,$contigs,$id) = $self->_rearrange([qw(SOURCE CONTIGS ID)], @args);
$self->{'_contigs'} = {};
$self->{'_singlets'} = {};
$self->{'_seqs'} = {};
$self->{'_annotation'} = Bio::Annotation::Collection->new();
$self->{'_id'} = 'NoName';
if (defined $contigs && ref($contigs = 'ARRAY')) {
foreach my $contig (@{$contigs}) {
$self->add_contig($contig);
}
}
$self->{'_id'} = $id if (defined $id);
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 = shift;
my $id = shift;
$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 assembly
Returns : integer
Args : none
=cut
sub get_nof_contigs {
my $self = shift;
return scalar( $self->get_contig_ids() );
}
=head2 get_nof_sequences_in_contigs
Title : get_nof_sequences_in_contigs
Usage : $assembly->get_nof_sequences_in_contigs()
Function:
Get the number of sequences included in the
assembly. This number refers only to the sequences used
to build contigs in this assembly. It does not includes
contig consensus sequences or singlets.
Returns : integer
Args : none
=cut
sub get_nof_sequences_in_contigs {
my $self = shift;
my $nof_seqs = 0;
foreach my $contig ($self->all_contigs) {
$nof_seqs += scalar( $contig->get_seq_ids() );
}
return $nof_seqs;
}
=head2 get_nof_singlets
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() );
}
=head2 get_seq_ids
Title : get_seq_ids
Usage : $assembly->get_seq_ids()
Function:
Get the ID of sequences from all contigs. This list
refers only to the aligned sequences in contigs. It does
not includes contig consensus sequences or singlets.
Returns : array of strings
Args : none
=cut
sub get_seq_ids {
my $self = shift;
return keys %{ $self->{'_seqs'} };
}
=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 $self = shift;
return sort keys %{$self->{'_contigs'}};
}
=head2 get_singlet_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 $self = shift;
return sort keys %{$self->{'_singlets'}};
}
=head2 get_seq_by_id
Title : get_seq_by_id
Usage : $assembly->get_seq_by_id($id)
Function:
Get a reference for an aligned sequence
This sequence must be part of a contig
in the assembly.
Returns : a Bio::LocatableSeq object
undef if sequence $id is not found
in any contig
Args : [string] sequence identifier (id)
=cut
sub get_seq_by_id {
my $self = shift;
my $seqID = shift;
return undef 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 undef 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::PrimarySeqI object or undef
Args : [string] a singlet ID
=cut
sub get_singlet_by_id {
my $self = shift;
my $singletID = shift;
return undef 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 = shift;
my $contig = shift;
if( !ref $contig || ! $contig->isa('Bio::Assembly::Contig') ) {
$self->throw("Unable to process non Bio::Assembly::Contig object [", ref($contig), "]");
}
my $contigID = $contig->id();
if( !defined $contigID ) {
$contigID = 'Unknown_' . ($self->get_nof_contigs() + 1);
$contig->id($contigID);
$self->warn("Attributing ID $contigID to unidentified Bio::Assembly::Contig object.");
}
$self->warn("Replacing contig $contigID with a new contig object")
if (exists $self->{'_contigs'}{$contigID});
$self->{'_contigs'}{$contigID} = $contig;
foreach my $seqID ($contig->get_seq_ids()) {
if (exists $self->{'_seqs'}{$seqID}) {
$self->warn( "Sequence $seqID already assigned to contig ".
$self->{'_seqs'}{$seqID}->id().". Moving to contig $contigID")
unless ($self->{'_seqs'}{$seqID} eq $contig);
}
$self->{'_seqs'}{$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, 0 otherwise
Args : a Bio::PrimarySeqI object
order (optional)
=cut
sub add_singlet {
my $self = shift;
my $singlet = shift;
if( !ref $singlet || ! $singlet->isa('Bio::PrimarySeqI') ) {
$self->warn("Unable to process non Bio::SeqI object [", ref($singlet), "]");
return 0;
}
my $singletID = $singlet->id();
$self->warn("Replacing singlet $singletID wih a new sequence object")
if (exists $self->{'_contigs'}{$singletID});
$self->{'_singlets'}{$singletID} = $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 : nothing
Args : none
=cut
sub update_seq_list {
my $self = shift;
$self->{'_seqs'} = {};
foreach my $contig ($self->all_contigs) {
foreach my $seqID ($contig->get_seq_ids) {
$self->{'_seqs'}{$seqID} = $contig;
}
}
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 : $assembly->remove_singlets(@singlet_ids)
Function: Remove singlet from assembly object
Returns : the Bio::SeqI objects removed
Args : a list of singlet IDs
See function get_singlet_ids() above
=cut
#---------------------
sub remove_singlets {
#---------------------
my ($self,@args) = @_;
my @ret = ();
foreach my $singletID (@args) {
push(@ret,$self->{'_singlets'}{$singletID});
delete $self->{'_singlets'}{$singletID};
}
return @ret;
}
=head1 Contig and singlet selection methos
=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 : $assembly->select_singlets(@list)
Function: Selects an array of singlets from the assembly
Returns : an array of Bio::SeqI objects
Args : an array of singlet ids
See function get_singlet_ids() above
=cut
#---------------------
sub select_singlets {
#---------------------
my ($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 = $assembly->all_singlets
Function:
Returns a list of all singlets in this assembly.
Singlets are isolated reads, without non-vector
matches to any other read in the assembly.
Returns : array of Bio::SeqI (in lexical order by id)
Args : none
=cut
#---------------------
sub all_singlets {
#---------------------
my ($self) = @_;
my @singlets = ();
foreach my $singlet (sort { $a cmp $b } keys %{ $self->{'_singlets'} }) {
push(@singlets, $self->{'_singlets'}{$singlet});
}
return @singlets;
}
# =head1 Internal Methods
1;
]]>