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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, "\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    :