Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies

SYNOPSIS

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    # get a Bio::Assembly::ScaffoldI object somehow

    foreach my $contig ($assembly->all_contigs) {
       # do something (see Bio::Assembly::Contig)
    }

DESCRIPTION

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This interface defines the basic set of methods an object should have to manipulate assembly data.

FEEDBACK

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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

Support

Please direct usage questions or support issues to the mailing list:

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.

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/

AUTHOR - Robson Francisco de Souza

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Email: rfsouza@citri.iq.usp.br

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Accessing general assembly data

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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

get_nof_singlets

	Title   : get_nof_singlets
	Usage   : $assembly->get_nof_singlets()
	Function: Get the number of singlets included in the assembly
	Returns : integer
	Args    : none

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.
                  undef otherwise
	Args    : an array of contig IDs

get_singlet_ids

	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

get_contig_by_id

    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)

get_singlet_by_id

    Title   : get_singlet_by_id
    Usage   : $assembly->get_singlet_by_id()
    Function: Get a reference for a singlet from the assembly
    Returns : Bio::Assembly::Singlet object or undef
    Args    : [string] a singlet ID

Modifier methods

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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.

add_contig

	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

add_singlet

	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::Assembly::Singlet object

remove_contigs

        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

remove_singlets

        Title   : remove_singlets
	Usage   : $assembly->remove_singlets(1..4)
	Function: Remove singlets from assembly object
	Returns : an array of Bio::Assembly::Singlet objects
	Args    : an array of singlet IDs 

    See function get_singlet_ids() above

Contig and singlet selection methos

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select_contigs

	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

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

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
	Args    : none

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
    Args    : none
BioPerl documentation Contained in the BioPerl distribution. 
#
#  BioPerl module for Bio::Assembly::ScaffoldI
#
# 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


#
# Now, let's code!


package Bio::Assembly::ScaffoldI;

use strict;
use Carp;

# Inheritance

use base qw(Bio::Root::RootI);

#
# Methods


sub get_nof_contigs {
    my $self = shift;

    $self->throw_not_implemented();
}


sub get_nof_singlets {
    my $self = shift;

    $self->throw_not_implemented();
}


sub get_contig_ids {
    my $self = shift;

    $self->throw_not_implemented();
}


sub get_singlet_ids {
    my $self = shift;

    $self->throw_not_implemented();
}


sub get_contig_by_id {
    my $self = shift;
    $self->throw_not_implemented();
}


sub get_singlet_by_id {
    my $self = shift;
    $self->throw_not_implemented();
}


#---------------------
sub add_contig {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}


#---------------------
sub add_singlet {
#---------------------
	my ($self) = @_;
	$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();
}


#---------------------
sub all_contigs {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}


#---------------------
sub all_singlets {
#---------------------
	my ($self) = @_;
	$self->throw_not_implemented();
}

1;