Bio::Assembly
ScaffoldI
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Summary
Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
No synopsis!
Description
This interface defines the basic set of methods an object should have
to manipulate assembly data.
Methods
Methods description
Title : add_contig
Usage : $assembly->add_contig($contig)
Function: Add another contig to the Bio::Assembly::ScaffoldI object
Returns : 1 on success, 0 otherwise
Args : a Bio::Assembly:Contig object
See Bio::Assembly::Contig for more information |
Title : add_singlet
Usage : $assembly->add_singlet($seq)
Function: Add another singlet to the Bio::Assembly::ScaffoldI object
Returns : 1 on success, 0 otherwise
Args : a Bio::Align::Singlet object |
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
Args : none |
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::Contig
Args : none |
Title : get_contig_by_id
Usage : $assembly->get_contig_by_id($id)
Function: Get a reference for a contig from the assembly
Returns : a Bio::Assembly::Contig object or undef
Args : [string] contig unique identifier (ID) |
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.
undef otherwise
Args : an array of contig IDs |
Title : get_nof_contigs
Usage : $assembly->get_nof_contigs()
Function: Get the number of contigs included in the assembly
Returns : integer
Args : none |
Title : get_nof_singlets
Usage : $assembly->get_nof_singlets()
Function: Get the number of singlets included in the assembly
Returns : integer
Args : none |
Title : get_singlet_by_id
Usage : $assembly->get_singlet_by_id()
Function: Get a reference for a singlet from the assembly
Returns : Bio::PrimarySeqI object or undef
Args : [string] a singlet ID |
Title : get_singlet_ids
Usage : $assembly->get_singlet_ids()
Function: Access list of singlet IDs from assembly
Returns : an array if there are any singlets in the assembly.
undef otherwise
Args : an array of singlet IDs |
Title : remove_contigs
Usage : $assembly->remove_contigs(1..4)
Function: Remove contig from assembly object
Returns : a Bio::Assembly::Contig object
Args : a list of contig IDs
See function get_contig_ids() above |
Title : remove_singlets
Usage : $assembly->remove_singlets(1..4)
Function: Remove singlet from assembly object
Returns : a Bio::SeqI object
Args : a list of singlet IDs
See function get_singlet_ids() above |
Title : select_contig
Usage : $assembly->select_contig
Function: Selects 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 |
Title : select_singlets
Usage : $assembly->select_singlets(@list)
Function: Selects an array of singlets from the assembly
Returns : an array of Bio::SeqI objects
Args : an array of singlet ids
See function get_singlet_ids() above |
Methods code
sub add_contig
{
my ($self) = @_;
$self->throw_not_implemented();
} | sub add_singlet
{
my ($self) = @_;
$self->throw_not_implemented();
} | sub all_contigs
{
my ($self) = @_;
$self->throw_not_implemented();
} | sub all_singlets
{
my ($self) = @_;
$self->throw_not_implemented();
}
1;
} | sub get_contig_by_id
{ my $self = shift;
$self->throw_not_implemented();} | sub get_contig_ids
{ my $self = shift;
$self->throw_not_implemented();} | sub get_nof_contigs
{ my $self = shift;
$self->throw_not_implemented();} | sub get_nof_singlets
{ my $self = shift;
$self->throw_not_implemented();} | sub get_singlet_by_id
{ my $self = shift;
$self->throw_not_implemented();} | sub get_singlet_ids
{ my $self = shift;
$self->throw_not_implemented();} | sub remove_contigs
{
my ($self) = @_;
$self->throw_not_implemented();
} | sub remove_singlets
{
my ($self) = @_;
$self->throw_not_implemented();
} | sub select_contigs
{
my ($self) = @_;
$self->throw_not_implemented();
} | sub select_singlets
{
my ($self) = @_;
$self->throw_not_implemented();
} | General documentation
# get a Bio::Assembly::ScaffoldI object somehow
foreach my $contig ($assembly->all_contigs) {
# do something (see Bio::Assembly::Contig)
}
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| AUTHOR - Robson Francisco de Souza | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
| Accessing general assembly data | Top |
Implementation of these methods is optional in the sense that
read-only implementations may not have these. If an object implements
one of them, it should however implement all.
| Contig and singlet selection methos | Top |