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Bio::NexmlIO(3)	      User Contributed Perl Documentation      Bio::NexmlIO(3)

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

perl v5.24.1			  2017-07-08		       Bio::NexmlIO(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chase Miller | CONTRIBUTORS | APPENDIX | CONSTRUCTOR | ITERATORS

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