Bio::Assembly::Scaffold(3pm)				User Contributed Perl Documentation			      Bio::Assembly::Scaffold(3pm)

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

perl v5.14.2							    2012-03-02					      Bio::Assembly::Scaffold(3pm)