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)