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

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:

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

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

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