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, "\n";

   print $aln->length, "\n";
   print $aln->no_residues, "\n";
   print $aln->is_flush, "\n";
   print $aln->no_sequences, "\n";

   $aln->splice_by_seq_pos(1);

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

   print "\n";
 }

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

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:

  http://bugzilla.open-bio.org/

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    :