| Bio::Assembly::ScaffoldI(3pm) | User Contributed Perl Documentation | Bio::Assembly::ScaffoldI(3pm) |
Bio::Assembly::ScaffoldI - Abstract Interface of Sequence Assemblies
# get a Bio::Assembly::ScaffoldI object somehow
foreach my $contig ($assembly->all_contigs) {
# do something (see Bio::Assembly::Contig)
}
This interface defines the basic set of methods an object should have to manipulate assembly data.
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
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:
https://github.com/bioperl/bioperl-live/issues
Email: rfsouza@citri.iq.usp.br
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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_singlets
Usage : $assembly->get_nof_singlets()
Function: Get the number of singlets included in the assembly
Returns : integer
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.
undef otherwise
Args : an array of contig 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
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)
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
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.
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
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
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
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
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
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
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
Args : none
| 2018-10-27 | perl v5.26.2 |