/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::AlignIO::maf

NAME

FAST::Bio::AlignIO::maf - Multiple Alignment Format sequence input stream

SYNOPSIS

Do not use this module directly.  Use it via the FAST::Bio::AlignIO class.

use FAST::Bio::AlignIO;

my $alignio = FAST::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 FAST::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:

https://redmine.open-bio.org/projects/bioperl/

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 = FAST::Bio::AlignIO->new(-format => 'maf'
					  -file   => '>file',
					  -idlength => 10,
					  -idlinebreak => 1);
 Function: Initialize a new L<FAST::Bio::AlignIO::maf> reader
 Returns : L<FAST::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<FAST::Bio::SimpleAlign> object
Args    :