Bio::AlignIO::maf(3)

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->num_residues, "\n";
   print $aln->is_flush, "\n";
   print $aln->num_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

  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:

  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    :