---
name: "Bio::AlignIO::metafasta"
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::metafasta"
---

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

Metafasta MSA Sequence input/output stream

## NAME

Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream

## SYNOPSIS

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

## DESCRIPTION

This object can transform Bio::SimpleAlign objects to and from metafasta flat file databases.

The format of a metafasta file is

```
  >test/1-25
  ABCDEFHIJKLMNOPQRSTUVWXYZ
  &charge
  NBNAANCNJCNNNONNCNNUNNXNZ
  &chemical
  LBSAARCLJCLSMOIMCHHULRXRZ
```

where the sequence block is followed by one or several meta blocks. Each meta block starts with the ampersand character '&' in the first column and is immediately followed by the name of the meta data which continues until the new line. The meta data follows it. All characters, except new line, are important in meta data.

## SEE ALSO

Bio::SeqIO::metafasta

## 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
```

## AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

## APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_

### next\_aln

```
 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
            or on error
 Args    : NONE
```

### write\_aln

```
 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in fasta format
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object
```

### width

```
 Title   : width
 Usage   : $obj->width($newval)
 Function: Get/Set the line width for METAFASTA output
 Returns : value of width
 Args    : newvalue (optional)
```