Bio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies # get a Bio::Assembly::ScaffoldI object somehow foreach my $contig ($assembly->all_contigs) { # do something (see Bio::Assembly::Contig) } This interface defines the basic set of methods an object should have to manipulate assembly data.

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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/ Email: rfsouza@citri.iq.usp.br The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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::PrimarySeqI object or undef Args : [string] a singlet ID 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::Align::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 singlet from assembly object Returns : a Bio::SeqI object Args : a list of singlet IDs See function get_singlet_ids() above

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::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 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::Contig Args : none