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

NAME

       Bio::AlignIO::maf - Multiple Alignment Format sequence input stream

SYNOPSIS

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

	use Bio::AlignIO;

	my $alignio = Bio::AlignIO->new(-fh => *STDIN, -format => 'maf');

	while(my $aln = $alignio->next_aln()){
	  my $match_line = $aln->match_line;

	  print $aln, "
";

	  print $aln->length, "
";
	  print $aln->num_residues, "
";
	  print $aln->is_flush, "
";
	  print $aln->num_sequences, "
";

	  $aln->splice_by_seq_pos(1);

	  print $aln->consensus_string(60), "
";
	  print $aln->get_seq_by_pos(1)->seq, "
";
	  print $aln->match_line(), "
";

	  print "
";
	}

DESCRIPTION

       This class constructs Bio::SimpleAlign objects from an MAF-format multiple alignment file.

       Writing in MAF format is currently unimplemented.

       Spec of MAF format is here:
	 http://genome.ucsc.edu/FAQ/FAQformat

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 - Allen Day
       Email: allenday@ucla.edu

APPENDIX

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

   new
	Title	: new
	Usage	: my $alignio = Bio::AlignIO->new(-format => 'maf'
						 -file	 => '>file',
						 -idlength => 10,
						 -idlinebreak => 1);
	Function: Initialize a new L<Bio::AlignIO::maf> reader
	Returns : L<Bio::AlignIO> object
	Args	:

   next_aln
	Title	: next_aln
	Usage	: $aln = $stream->next_aln()
	Function: returns the next alignment in the stream.
		  Throws an exception if trying to read in PHYLIP
		  sequential format.
	Returns : L<Bio::SimpleAlign> object
	Args	:

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