Bio::AlignIO::nexus(3pm) User Contributed Perl Documentation Bio::AlignIO::nexus(3pm)
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://redmine.open-bio.org/projects/bioperl/
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 v5.14.2 2012-03-02 Bio::AlignIO::nexus(3pm)