---
name: "Bio::AlignIO::selex"
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::selex"
---

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

selex sequence input/output stream

## NAME

Bio::AlignIO::selex - selex sequence input/output stream

## SYNOPSIS

```
  # Do not use this module directly.  Use it via the L<Bio::AlignIO> class.
  use Bio::AlignIO;
  use strict;
  my $in = Bio::AlignIO->new(-format => 'selex',
                             -file   => 't/data/testaln.selex');
  while( my $aln = $in->next_aln ) {
  }
```

## DESCRIPTION

This object can transform Bio::Align::AlignI objects to and from selex flat file databases.

## 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 - Peter Schattner

Email: schattner@alum.mit.edu

## CONTRIBUTORS

Jason Stajich, jason-at-bioperl.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. Tries to read *all* selex
          It reads all non whitespace characters in the alignment
          area. For selexs with weird gaps (eg ~~~) map them by using
          $al->map_chars('~','-')
 Returns : L<Bio::Align::AlignI> object
 Args    : NONE
```

### write\_aln

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