Christopher Fields > BioPerl-1.6.921 > Bio::AlignIO::po

Download:
BioPerl-1.6.921.tar.gz

Dependencies

Annotate this POD

CPAN RT

New  9
Open  4
View/Report Bugs
Module Version: 1.006921   Source   Latest Release: BioPerl-1.6.923

NAME ^

Bio::AlignIO::po - po MSA Sequence input/output stream

SYNOPSIS ^

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

DESCRIPTION ^

This object can transform Bio::SimpleAlign objects to and from 'po' format flat file databases. 'po' format is the native format of the POA alignment program (Lee C, Grasso C, Sharlow MF, 'Multiple sequence alignment using partial order graphs', Bioinformatics (2002), 18(3):452-64).

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 - Matthew Betts ^

Email: matthew.betts@ii.uib.no

APPENDIX ^

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

next_aln

 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : L<Bio::Align::AlignI> object - returns undef on end of file
            or on error
 Args    : NONE

write_aln

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in po format
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object
syntax highlighting: