Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Assembly::Scaffold - Perl module to hold and manipulate sequence assembly data.

SYNOPSIS # # Module loading use Bio::Assembly::IO;

           # Assembly loading methods
           my $aio = Bio::Assembly::IO->new(-file=>"test.ace.1", -format=>'phrap');
           my $assembly = $aio->next_assembly;

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

DESCRIPTION

       Bio::Assembly::Scaffold was developed to store and manipulate data from sequence assembly
       programs like Phrap. It implements the ScaffoldI interface and intends to be generic
       enough to be used by Bio::Assembly::IO drivers written to programs other than Phrap.

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:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Robson Francisco de Souza

       rfsouza@citri.iq.usp.br

APPENDIX

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

   new ()
           Title   : new
           Usage   : $scaffold = new ( -id       => "assembly 1",
                                       -source   => 'program_name',
                                       -contigs  => \@contigs,
                                       -singlets => \@singlets );
           Function: creates a new scaffold object
           Returns : Bio::Assembly::Scaffold
           Args    : -id       : [string] scaffold name
                     -source   : [string] sequence assembly program
                     -contigs  : reference to array of Bio::Assembly::Contig objects
                     -singlets : reference to array of Bio::Assembly::Singlet objects

Accessing general assembly data

   id
           Title   : id
           Usage   : $assembly->id()
           Function: Get/Set assembly ID
           Returns : string or undef
           Args    : string

   annotation
           Title   : annotation
           Usage   : $assembly->annotation()
           Function: Get/Set assembly annotation object
           Returns : Bio::Annotation::Collection
           Args    : none

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

   get_nof_contig_seqs
           Title   : get_nof_contig_seqs
           Usage   : $assembly->get_nof_contig_seqs()
           Function: Get the number of sequences included in contigs of the
                     scaffold (no consensus sequences or singlets)
           Returns : integer
           Args    : none

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

   get_all_seq_ids
           Title   : get_all_seq_ids
           Usage   : $assembly->get_all_seq_ids()
           Function: Get the ID of all sequences making up the scaffold
                     (sequences from contigs and singlets, not consensus).
           Returns : array of strings
           Args    : none

   get_nof_seqs
           Title   : get_nof_seqs
           Usage   : $assembly->get_nof_seqs()
           Function: Get total number of sequences making up the scaffold
                     (sequences from contigs and singlets, not consensus).
           Returns : integer
           Args    : none

   get_contig_seq_ids
           Title   : get_contig_seq_ids
           Usage   : $assembly->get_contig_seq_ids()
           Function: Get the ID of all sequences in contigs
           Returns : array of strings
           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. An empty array otherwise
           Args    : none

   get_singlet_ids (get_singlet_seq_ids)
           Title   : get_singlet_ids
           Usage   : $assembly->get_singlet_ids()
           Function: Access list of singlet IDs from assembly
           Returns : array of strings if there are any singlets
                     otherwise an empty array
           Args    : none

   get_seq_by_id
           Title   : get_seq_by_id
           Usage   : $assembly->get_seq_by_id($id)
           Function: Get a reference for an sequence making up the scaffold
                     (from a contig or singlet, not consensus)
           Returns : a Bio::LocatableSeq object
                     undef if sequence $id is not found in the scaffold
           Args    : [string] sequence identifier (id)

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

Modifier methods

   add_contig
           Title   : add_contig
           Usage   : $assembly->add_contig($contig)
           Function: Add a contig to the assembly
           Returns : 1 on success
           Args    : a Bio::Assembly::Contig object
                 order (optional)

   add_singlet
           Title   : add_singlet
           Usage   : $assembly->add_singlet($seq)
           Function: Add a singlet to the assembly
           Returns : 1 on success
           Args    : a Bio::Assembly::Singlet object
                     order (optional)

   update_seq_list
           Title   : update_seq_list
           Usage   : $assembly->update_seq_list()
           Function:

                     Synchronizes the assembly registry for sequences in
                     contigs and contig actual aligned sequences content. You
                     probably want to run this after you remove/add a
                     sequence from/to a contig in the assembly.

           Returns : 1 for success
           Args    : none

   remove_contigs
           Title   : remove_contigs
           Usage   : $assembly->remove_contigs(1..4)
           Function: Remove contig from assembly object
           Returns : an array of removed Bio::Assembly::Contig
                     objects
           Args    : an array of contig IDs

           See function get_contig_ids() above

   remove_singlets
           Title   : remove_singlets
           Usage   : $assembly->remove_singlets(@singlet_ids)
           Function: Remove singlet from assembly object
           Returns : the Bio::Assembly::Singlet objects removed
           Args    : a list of singlet IDs

           See function get_singlet_ids() above

   remove_features_collection
           Title   : remove_features_collection
           Usage   : $assembly->remove_features_collection()
           Function: Removes the collection of features associated to every
                     contig and singlet of the scaffold. This can be useful
                     to save some memory (when contig and singlet features are
                     not needed).
           Returns   : none
           Argument  : none

Contig and singlet selection methods

   select_contigs
           Title   : select_contigs
           Usage   : $assembly->select_contigs(@list)
           Function: Select 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 (in lexical id order)
           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 (in lexical order by id)
           Args    : none