Bio::NexmlIO(3pm) User Contributed Perl Documentation Bio::NexmlIO(3pm)
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 <http://www.nexml.org>.
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://redmine.open-bio.org/projects/bioperl/
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<Bio::NexmlIO> object linked to a stream
Returns : a L<Bio::NexmlIO> object
Args : file name
See L<Bio::Root::IO>
doc
Title : doc
Usage : my $nexml_doc = $in_nexmlIO->doc();
Function: returns a L<Bio::Phylo::Project> object that contains all the Bio::Phylo data objects parsed from the stream
Returns : a L<Bio::Phylo::Project> 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<Bio::Tree::Tree> 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<Bio::Seq> 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<Bio::SimpleAlign> 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<Bio::Seq>, @L<Bio::SimpleAlign>, @L<Bio::Tree::Tree>
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<Bio::SeqIO> 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<Bio::AlignIO> 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<Bio::TreeIO> to do
the conversion and writing.
Returns : none
Args : file to write to, format to be converted to
See Bio::Tree::Tree, Bio::TreeIO
perl v5.14.2 2012-03-02 Bio::NexmlIO(3pm)