NAME

Bio::AlignIO::maf - Multipla 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://hgwdev-sugnet.cse.ucsc.edu/cgi-bin/hgGateway?org=human

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.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 = new Bio::AlignIO(-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    :