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.\" ========================================================================
.\"
.IX Title "Bio::Assembly::Scaffold 3pm"
.TH Bio::Assembly::Scaffold 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::Assembly::Scaffold \- Perl module to hold and manipulate sequence assembly
data.
.SH "SYNOPSIS # # Module loading use Bio::Assembly::IO;"
.IX Header "SYNOPSIS # # Module loading use Bio::Assembly::IO;"
.Vb 3
\&    # Assembly loading methods
\&    my $aio = Bio::Assembly::IO\->new(\-file=>"test.ace.1", \-format=>\*(Aqphrap\*(Aq);
\&    my $assembly = $aio\->next_assembly;
\&
\&    foreach my $contig ($assembly\->all_contigs) {
\&        # do something... (see Bio::Assembly::Contig)
\&    }
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Robson Francisco de Souza"
.IX Header "AUTHOR - Robson Francisco de Souza"
rfsouza@citri.iq.usp.br
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "new ()"
.IX Subsection "new ()"
.Vb 11
\&    Title   : new
\&    Usage   : $scaffold = new ( \-id       => "assembly 1",
\&                                \-source   => \*(Aqprogram_name\*(Aq,
\&                                \-contigs  => \e@contigs,
\&                                \-singlets => \e@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
.Ve
.SH "Accessing general assembly data"
.IX Header "Accessing general assembly data"
.SS "id"
.IX Subsection "id"
.Vb 5
\&    Title   : id
\&    Usage   : $assembly\->id()
\&    Function: Get/Set assembly ID
\&    Returns : string or undef
\&    Args    : string
.Ve
.SS "annotation"
.IX Subsection "annotation"
.Vb 5
\&    Title   : annotation
\&    Usage   : $assembly\->annotation()
\&    Function: Get/Set assembly annotation object
\&    Returns : Bio::Annotation::Collection
\&    Args    : none
.Ve
.SS "get_nof_contigs"
.IX Subsection "get_nof_contigs"
.Vb 5
\&    Title   : get_nof_contigs
\&    Usage   : $assembly\->get_nof_contigs()
\&    Function: Get the number of contigs included in the scaffold
\&    Returns : integer
\&    Args    : none
.Ve
.SS "get_nof_contig_seqs"
.IX Subsection "get_nof_contig_seqs"
.Vb 6
\&    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
.Ve
.SS "get_nof_singlets (get_nof_singlet_seqs)"
.IX Subsection "get_nof_singlets (get_nof_singlet_seqs)"
.Vb 5
\&    Title   : nof_singlets
\&    Usage   : $assembly\->nof_singlets()
\&    Function: Get the number of singlets included in the assembly
\&    Returns : integer
\&    Args    : none
.Ve
.SS "get_all_seq_ids"
.IX Subsection "get_all_seq_ids"
.Vb 6
\&    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
.Ve
.SS "get_nof_seqs"
.IX Subsection "get_nof_seqs"
.Vb 6
\&    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
.Ve
.SS "get_contig_seq_ids"
.IX Subsection "get_contig_seq_ids"
.Vb 5
\&    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
.Ve
.SS "get_contig_ids"
.IX Subsection "get_contig_ids"
.Vb 6
\&    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
.Ve
.SS "get_singlet_ids (get_singlet_seq_ids)"
.IX Subsection "get_singlet_ids (get_singlet_seq_ids)"
.Vb 6
\&    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
.Ve
.SS "get_seq_by_id"
.IX Subsection "get_seq_by_id"
.Vb 7
\&    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)
.Ve
.SS "get_contig_by_id"
.IX Subsection "get_contig_by_id"
.Vb 5
\&    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)
.Ve
.SS "get_singlet_by_id"
.IX Subsection "get_singlet_by_id"
.Vb 5
\&    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
.Ve
.SH "Modifier methods"
.IX Header "Modifier methods"
.SS "add_contig"
.IX Subsection "add_contig"
.Vb 6
\&    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)
.Ve
.SS "add_singlet"
.IX Subsection "add_singlet"
.Vb 6
\&    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)
.Ve
.SS "update_seq_list"
.IX Subsection "update_seq_list"
.Vb 3
\&    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
.Ve
.SS "remove_contigs"
.IX Subsection "remove_contigs"
.Vb 6
\&    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
.Ve
.SS "remove_singlets"
.IX Subsection "remove_singlets"
.Vb 5
\&    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
.Ve
.SS "remove_features_collection"
.IX Subsection "remove_features_collection"
.Vb 8
\&    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
.Ve
.SH "Contig and singlet selection methods"
.IX Header "Contig and singlet selection methods"
.SS "select_contigs"
.IX Subsection "select_contigs"
.Vb 5
\&    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
.Ve
.SS "select_singlets"
.IX Subsection "select_singlets"
.Vb 5
\&    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
.Ve
.SS "all_contigs"
.IX Subsection "all_contigs"
.Vb 3
\&    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
.Ve
.SS "all_singlets"
.IX Subsection "all_singlets"
.Vb 3
\&    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
.Ve