---
name: "Bio::Assembly::Singlet"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.2-3"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::Assembly::Singlet"
---

# Bio::Assembly::Singlet(3pm)

Perl module to hold and manipulate singlets from sequence assembly contigs.

## NAME

Bio::Assembly::Singlet - Perl module to hold and manipulate\
                      singlets from sequence assembly contigs.

## SYNOPSIS

```
    # Module loading
    use Bio::Assembly::IO;
    # Assembly loading methods
    $aio = Bio::Assembly::IO->new( -file   => 'test.ace.1',
                                   -format => 'phrap'      );
    $assembly = $aio->next_assembly;
    foreach $singlet ($assembly->all_singlets) {
      # do something
    }
    # OR, if you want to build the singlet yourself,
    use Bio::Assembly::Singlet;
    $singlet = Bio::Assembly::Singlet->new(
        -id     => 'Singlet1',
        -seqref => $seq
    );
```

## DESCRIPTION

A singlet is a sequence that phrap was unable to align to any other sequences.

## FEEDBACK

### Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists  Your participation is much appreciated.

```
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
```

### 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 - Chad S. Matsalla

bioinformatics1 at dieselwurks.com

## APPENDIX

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

### new

```
    Title   : new
    Usage   : $singlet = $io->new( -seqref => $seq )
    Function: Create a new singlet object
    Returns : A Bio::Assembly::Singlet object
    Args    : -seqref => Bio::Seq-compliant sequence object for the singlet
```

### seqref

```
    Title   : seqref
    Usage   : $seqref = $singlet->seqref($seq);
    Function: Get/set the sequence to which this singlet refers
    Returns : A Bio::Seq-compliant object
    Args    : A Bio::Seq-compliant or Bio::Seq::Quality object
```

### \_seq\_to\_singlet

```
    Title   : _seq_to_singlet
    Usage   : $singlet->seqref($seq)
    Function: Transform a sequence into a singlet
    Returns : 1 for success
    Args    : A Bio::Seq-compliant object
```