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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:

   http://bugzilla.open-bio.org/
 
 

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