Bio::Assembly::ScaffoldI(3)

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

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

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

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

FEEDBACK

  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:

  http://bugzilla.open-bio.org/

AUTHOR - Robson Francisco de Souza
Email: rfsouza@citri.iq.usp.br

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

Accessing general assembly data

  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
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

  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