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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : id Usage : $assembly->id() Function: Get/Set assembly ID Returns : string or undef Args : string
Title : annotation Usage : $assembly->annotation() Function: Get/Set assembly annotation object Returns : Bio::Annotation::Collection Args : none
Title : get_nof_contigs Usage : $assembly->get_nof_contigs() Function: Get the number of contigs included in the assembly Returns : integer Args : none
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
Title : nof_singlets Usage : $assembly->nof_singlets() Function: Get the number of singlets included in the assembly Returns : integer Args : none
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
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
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
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)
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)
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
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)
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)
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
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
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
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
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
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
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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.