debian man page for bio::alignio::emboss

Bio::AlignIO::emboss(3pm)				User Contributed Perl Documentation				 Bio::AlignIO::emboss(3pm)

NAME
       Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)

SYNOPSIS
	   # do not use the object directly
	   use Bio::AlignIO;
	   # read in an alignment from the EMBOSS program water
	   my $in = Bio::AlignIO->new(-format => 'emboss',
				     -file   => 'seq.water');
	   while( my $aln = $in->next_aln ) {
	   # do something with the alignment
	   }

DESCRIPTION
       This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite.

FEEDBACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

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 0 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 emboss format
	Returns : 1 for success and 0 for error
	Args	: L<Bio::Align::AlignI> object

perl v5.14.2							    2012-03-02						 Bio::AlignIO::emboss(3pm)