Linux Certif

Toute la documentation sur la certification Linux LPI

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->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    :