/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::NexmlIO

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://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<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