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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 = new Bio::Assembly::IO(-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
 
 

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

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

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 assembly
     Returns : integer
     Args    : none
 
 

get_nof_sequences_in_contigs

     Title   : get_nof_sequences_in_contigs
     Usage   : $assembly->get_nof_sequences_in_contigs()
     Function: 
 
               Get the number of sequences included in the
               assembly. This number refers only to the sequences used
               to build contigs in this assembly. It does not includes
               contig consensus sequences or singlets.
 
     Returns : integer
     Args    : none
 
 

get_nof_singlets

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

get_seq_ids

     Title   : get_seq_ids
     Usage   : $assembly->get_seq_ids()
     Function: 
 
               Get the ID of sequences from all contigs.  This list
               refers only to the aligned sequences in contigs. It does
               not includes contig consensus sequences or singlets.
 
     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

     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 aligned sequence
               This sequence must be part of a contig
               in the assembly.
 
     Returns : a Bio::LocatableSeq object
               undef if sequence $id is not found
               in any contig
     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::PrimarySeqI 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, 0 otherwise
     Args    : a Bio::PrimarySeqI 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 : nothing
     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::SeqI objects removed
     Args    : a list of singlet IDs
 
     See function get_singlet_ids() above
 
 

Contig and singlet selection methos

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::SeqI 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::SeqI (in lexical order by id)
     Args    : none