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Man Pages
Bio::Assembly::ScaffoldI(3) User Contributed Perl Documentation Bio::Assembly::ScaffoldI(3)
 

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

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

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

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

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.

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

Email: rfsouza@citri.iq.usp.br

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

        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_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_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   : 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_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

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.

        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::Assembly::Singlet object

        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 singlets from assembly object
        Returns : an array of Bio::Assembly::Singlet objects
        Args    : an array 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::Assembly::Singlet objects
        Args    : an array of singlet ids
    See function get_singlet_ids() above

        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::Singlet objects
    Args    : none
2019-01-01 perl v5.28.1

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