| Bio::Assembly::Scaffold(3pm) | User Contributed Perl Documentation | Bio::Assembly::Scaffold(3pm) |
Bio::Assembly::Scaffold - Perl module to hold and manipulate sequence assembly data.
# Assembly loading methods
my $aio = Bio::Assembly::IO->new(-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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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.
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:
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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 : $scaffold = new ( -id => "assembly 1",
-source => 'program_name',
-contigs => \@contigs,
-singlets => \@singlets );
Function: creates a new scaffold object
Returns : Bio::Assembly::Scaffold
Args : -id : [string] scaffold name
-source : [string] sequence assembly program
-contigs : reference to array of Bio::Assembly::Contig objects
-singlets : reference to array of Bio::Assembly::Singlet objects
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 scaffold
Returns : integer
Args : none
Title : get_nof_contig_seqs
Usage : $assembly->get_nof_contig_seqs()
Function: Get the number of sequences included in contigs of the
scaffold (no 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_all_seq_ids
Usage : $assembly->get_all_seq_ids()
Function: Get the ID of all sequences making up the scaffold
(sequences from contigs and singlets, not consensus).
Returns : array of strings
Args : none
Title : get_nof_seqs
Usage : $assembly->get_nof_seqs()
Function: Get total number of sequences making up the scaffold
(sequences from contigs and singlets, not consensus).
Returns : integer
Args : none
Title : get_contig_seq_ids
Usage : $assembly->get_contig_seq_ids()
Function: Get the ID of all sequences in contigs
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 sequence making up the scaffold
(from a contig or singlet, not consensus)
Returns : a Bio::LocatableSeq object
undef if sequence $id is not found in the scaffold
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::Assembly::Singlet 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
Args : a Bio::Assembly::Singlet 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 : 1 for success
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::Assembly::Singlet objects removed
Args : a list of singlet IDs
See function get_singlet_ids() above
Title : remove_features_collection
Usage : $assembly->remove_features_collection()
Function: Removes the collection of features associated to every
contig and singlet of the scaffold. This can be useful
to save some memory (when contig and singlet features are
not needed).
Returns : none
Argument : none
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::Assembly::Singlet 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::Assembly::Singlet objects (in lexical order by id)
Args : none
| 2018-10-27 | perl v5.26.2 |