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Bio::AlignIO::nexus(3)User Contributed Perl DocumentatioBio::AlignIO::nexus(3)

NAME
       Bio::AlignIO::nexus - NEXUS format sequence input/output	stream

SYNOPSIS
       Do not use this module directly.	 Use it	via the	Bio::AlignIO class.

	   use Bio::AlignIO;

	   my $in = Bio::AlignIO->new(-format => 'nexus',
				     -file   =>	'aln.nexus');
	   while( my $aln = $in->next_aln ) {
	       # do something with the alignment
	   }

DESCRIPTION
       This object can transform Bio::Align::AlignI objects to and from	NEXUS
       data blocks. See	method documentation for supported NEXUS features.

ACKNOWLEDGEMENTS
       Will Fisher has written an excellent standalone NEXUS format parser in
       Perl, readnexus.	A number of tricks were	adapted	from it.

FEEDBACK
   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

AUTHORS	- Heikki Lehvaslaiho
       Email: heikki-at-bioperl-dot-org

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   new
	Title	: new
	Usage	: $alignio = Bio::AlignIO->new(-format => 'nexus', -file => 'filename');
	Function: returns a new	Bio::AlignIO object to handle clustalw files
	Returns	: Bio::AlignIO::clustalw object
	Args	: -verbose => verbosity	setting	(-1,0,1,2)
		  -file	   => name of file to read in or with ">" - writeout
		  -fh	   => alternative to -file param - provide a filehandle
			      to read from/write to
		  -format  => type of Alignment	Format to process or produce

		  Customization	of nexus flavor	output

		  -show_symbols	=> print the symbols="ATGC" in the data	definition
				   (MrBayes does not like this)
				   boolean [default is 1]
		  -show_endblock => print an 'endblock;' at the	end of the data
				   (MyBayes does not like this)
				   boolean [default is 1]

   next_aln
	Title	: next_aln
	Usage	: $aln = $stream->next_aln()
	Function: Returns the next alignment in	the stream.

		  Supports the following NEXUS format features:
		  - The	file has to start with '#NEXUS'
		  - Reads in the name of the alignment from a comment
		    (anything after 'TITLE: ') .
		  - Sequence names can be given	in a taxa block, too.
		  - If matchchar notation is used, converts
		    them back to sequence characters.
		  - Does character conversions specified in the
		    NEXUS equate command.
		  - Sequence names of type 'Homo sapiens' and
		    Homo_sapiens are treated identically.

	Returns	: L<Bio::Align::AlignI>	object
	Args	:

   write_aln
	Title	: write_aln
	Usage	: $stream->write_aln(@aln)
	Function: Writes the $aln object into the stream in interleaved	NEXUS
		  format. Everything is	written	into a data block.
		  SimpleAlign methods match_char, missing_char and gap_char must be set
		  if you want to see them in the output.
	Returns	: 1 for	success	and 0 for error
	Args	: L<Bio::Align::AlignI>	object

   flag
	Title	: flag
	Usage	: $obj->flag($name,$value)
	Function: Get/Set a flag value
	Returns	: value	of flag	(a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

perl v5.32.1			  2019-12-07		Bio::AlignIO::nexus(3)

NAME | SYNOPSIS | DESCRIPTION | ACKNOWLEDGEMENTS | FEEDBACK | AUTHORS - Heikki Lehvaslaiho | APPENDIX

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