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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Robson Francisco de Souza

Email: [email protected]

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