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 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 = 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    :