Bio::Assembly::ScaffolUser)Contributed Perl DocumenBio::Assembly::ScaffoldI(3)NAMEBio::Assembly::ScaffoldI - Abstract Inteface of Sequence Assemblies
SYNOPSIS
# get a Bio::Assembly::ScaffoldI object somehow
foreach my $contig ($assembly->all_contigs) {
# do something (see Bio::Assembly::Contig)
}
DESCRIPTION
This interface defines the basic set of methods an object should have
to manipulate assembly data.
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:
http://bugzilla.open-bio.org/
AUTHOR - Robson Francisco de Souza
Email: rfsouza@citri.iq.usp.br
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Accessing general assembly data
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::Assembly::Singlet object or undef
Args : [string] a singlet ID
Modifier methods
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::Assembly::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 singlets from assembly object
Returns : an array of Bio::Assembly::Singlet objects
Args : an array of singlet IDs
See function get_singlet_ids() above
Contig and singlet selection methos
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::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
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
Args : none
perl v5.14.1 2011-07-22 Bio::Assembly::ScaffoldI(3)
