Bio::AlignIO::nexus - NEXUS format sequence input/output stream
Do not use this module directly. Use it via the Bio::AlignIO class.
This object can transform Bio::Align::AlignI objects to and from NEXUS data blocks. See method documentation for supported NEXUS features.
Will Fisher has written an excellent standalone NEXUS format parser in perl, readnexus. A number of tricks were adapted from it.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/
Email: heikki@ebi.ac.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
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
