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

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://bio.perl.org/MailList.html - 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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ rfsouza@citri.iq.usp.br 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

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

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

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