---
name: "Bio::AlignIO::maf"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::AlignIO::maf"
---

# Bio::AlignIO::maf(3pm)

Multiple Alignment Format sequence input stream

## 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    :
```