--- name: "Bio::NexmlIO" 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::NexmlIO" --- # Bio::NexmlIO(3pm) stream handler for NeXML documents ## NAME Bio::NexmlIO - stream handler for NeXML documents ## SYNOPSIS ``` #Instantiate a Bio::Nexml object and link it to a file my $in_nexml = Bio::Nexml->new(-file => 'nexml_doc.xml', -format => 'Nexml'); #Read in some data my $bptree1 = $in_nexml->next_tree(); my $bpaln1 = $in_nexml->next_aln(); my $bpseq1 = $in_nexml->next_seq(); #Use/manipulate data ... #Write data to nexml file my $out_nexml = Bio::Nexml->new(-file => '>new_nexml_doc.xml', -format => 'Nexml'); $out_nexml->to_xml(); ``` ## DESCRIPTION Bio::NexmlIO is an I/O handler for a NeXML document. A NeXML document can represent three different data types: simple sequences, alignments, and trees. NexmlIO has four main methods next\_tree, next\_seq, next\_aln, and write. NexmlIO returns bioperl seq, tree, and aln objects which can be manipulated then passed to the write method of a new NexmlIO instance to allow the creation of a NeXML document. Each bioperl object contains all the information necessary to recreate a Bio::Phylo::Taxa object, so each time a bioperl object is converted to a biophylo object, the bioperl object is checked to see if its associated taxa has already been created (against a hash using the NexmlIO\_ID and Taxa\_ID to create a unique string). If not, it is created; if so, that taxa object is used to link the Bio::Phylo tree or matrix. For more information on the NeXML format, see \. ## 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 one of 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 - Chase Miller Email chmille4@gmail.com ## CONTRIBUTORS Mark A. Jensen, maj -at- fortinbras -dot- com ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ ## CONSTRUCTOR ### new ``` Title : new Usage : my $in_nexmlIO = Bio::NexmlIO->new(-file => 'data.nexml.xml'); Function: Creates a L object linked to a stream Returns : a L object Args : file name See L ``` ### doc ``` Title : doc Usage : my $nexml_doc = $in_nexmlIO->doc(); Function: returns a L object that contains all the Bio::Phylo data objects parsed from the stream Returns : a L object Args : none ``` ## ITERATORS ### next\_tree ``` Title : next_tree Usage : $tree = $stream->next_tree Function: Reads the next tree object from the stream and returns it. Returns : a L object Args : none ``` See Bio::Root::IO, Bio::Tree::Tree ### next\_seq ``` Title : next_seq Usage : $seq = $stream->next_seq Function: Reads the next seq object from the stream and returns it. Returns : a L object Args : none ``` See Bio::Root::IO, Bio::Seq ### next\_aln ``` Title : next_aln Usage : $aln = $stream->next_aln Function: Reads the next aln object from the stream and returns it. Returns : a L object Args : none ``` See Bio::Root::IO, Bio::SimpleAlign ### rewind\_seq ``` Title : rewind_seq Usage : $stream->rewind_seq Function: Resets the stream for seqs Returns : none Args : none ``` See Bio::Root::IO, Bio::Seq ### rewind\_aln ``` Title : rewind_aln Usage : $stream->rewind_aln Function: Resets the stream for alns Returns : none Args : none ``` See Bio::Root::IO, Bio::Simple::Align ### rewind\_tree ``` Title : rewind_tree Usage : $stream->rewind_tree Function: Resets the stream for trees Returns : none Args : none ``` See Bio::Root::IO, Bio::tree::tree ### write ``` Title : write Usage : $stream->write(-alns => $alns,-seqs => $seqs,-trees => $trees) Function: converts BioPerl seq, tree, and aln objects into Bio::Phylo seq, tree, and aln objects, constructs a Bio::Phylo::Project object made up of the newly created Bio::Phylo objects, and writes the Bio::Phylo:Project object to the stream as a valid nexml document Returns : none Args : \@L, \@L, \@L ``` See Bio::Root::IO, Bio::tree::tree, Bio::Seq, Bio::SimpleAlign ### extract\_seqs ``` Title : extract_seqs Usage : $nexmlIO->extract_seqs(-file => ">$outfile", -format => $format) Function: converts BioPerl seqs stored in the NexmlIO object into the provided format and writes it to the provided file. Uses L to do the conversion and writing. Returns : none Args : file to write to, format to be converted to ``` See Bio::Seq, Bio::SeqIO ### extract\_alns ``` Title : extract_alns Usage : $nexmlIO->extract_alns(-file => ">$outfile", -format => $format) Function: converts BioPerl alns stored in the NexmlIO object into the provided format and writes it to the provided file. Uses L to do the conversion and writing. Returns : none Args : file to write to, format to be converted to ``` See Bio::SimpleAlign, Bio::AlignIO ### extract\_trees ``` Title : extract_trees Usage : $nexmlIO->extract_trees(-file => ">$outfile", -format => $format) Function: converts BioPerl trees stored in the NexmlIO object into the provided format and writes it to the provided file. Uses L to do the conversion and writing. Returns : none Args : file to write to, format to be converted to ``` See Bio::Tree::Tree, Bio::TreeIO