Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::AlignIO::maf(3)  User Contributed Perl Documentation 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:

	 https://github.com/bioperl/bioperl-live/issues

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	:

perl v5.32.1			  2019-12-07		  Bio::AlignIO::maf(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHORS - Allen Day | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::AlignIO::maf&sektion=3&manpath=FreeBSD+13.0-RELEASE+and+Ports>

home | help