--- name: "Bio::Assembly::ScaffoldI" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.2-3" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Assembly::ScaffoldI" --- # Bio::Assembly::ScaffoldI(3pm) Abstract Interface of Sequence Assemblies ## NAME Bio::Assembly::ScaffoldI - Abstract Interface 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: ``` https://github.com/bioperl/bioperl-live/issues ``` ## 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 ```