Bio::Assembly::Scaffold(3pm) User Contributed Perl Documentation 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 = 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)
}
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
Support
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.
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:
https://redmine.open-bio.org/projects/bioperl/
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 : $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
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 scaffold
Returns : integer
Args : none
get_nof_contig_seqs
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
get_nof_singlets (get_nof_singlet_seqs)
Title : nof_singlets
Usage : $assembly->nof_singlets()
Function: Get the number of singlets included in the assembly
Returns : integer
Args : none
get_all_seq_ids
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
get_nof_seqs
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
get_contig_seq_ids
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
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 (get_singlet_seq_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 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)
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::Assembly::Singlet 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
Args : a Bio::Assembly::Singlet 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 : 1 for success
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::Assembly::Singlet objects removed
Args : a list of singlet IDs
See function get_singlet_ids() above
remove_features_collection
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
Contig and singlet selection methods
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::Assembly::Singlet 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::Assembly::Singlet objects (in lexical order by id)
Args : none
perl v5.14.2 2012-03-02 Bio::Assembly::Scaffold(3pm)