---
name: "Bio::PopGen::IO::prettybase"
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::PopGen::IO::prettybase"
---

# Bio::PopGen::IO::prettybase(3pm)

Extract individual allele data from PrettyBase format

## NAME

Bio::PopGen::IO::prettybase - Extract individual allele data from PrettyBase format

## SYNOPSIS

Do not use directly, use through the Bio::PopGen::IO driver

## DESCRIPTION

This object will parse comma delimited PrettyBase output.  PrettyBase is defined by the SeattleSNPs http://pga.gs.washington.edu/

This is expected to be tab delimited (you can vary with the field\_delimiter flag SITE SAMPLE ALLELE1 ALLELE2

There are 2 initialization parameters, the delimiter (-field\_delimiter) \[default 'tab'\] and a boolean -no\_header which specifies if there is no header line to read in.  All lines starting with '#' will be skipped

## 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 list.  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 of the bugs and their resolution. Bug reports can be submitted via the web:

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

## AUTHOR - Jason Stajich

Email jason-at-bioperl.org

## CONTRIBUTORS

Matthew Hahn, matthew.hahn-at-duke.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 $obj = Bio::PopGen::IO::prettybase->new();
 Function: Builds a new Bio::PopGen::IO::prettybase object
 Returns : an instance of Bio::PopGen::IO::prettybase
 Args    : -field_delimiter      => a field delimiter character or regexp (default is /\t/ )
           -header               => boolean if the file will have a header and parser should
                                    skip first line in the file (default is false)
           -convert_indel_states => convert alleles which are longer than one character
                                    to an 'I' meaning insert state, and alleles which are
                                    '-' to a delete state.
                                    (default is false)
```

### flag

```
 Title   : flag
 Usage   : $obj->flag($flagname,$newval)
 Function: Get/Set the flag value
 Returns : value of a flag (a boolean)
 Args    : A flag name, currently we expect
           'header', 'field_delimiter', or 'allele_delimiter'
           on set, new value (a boolean or undef, optional)
```

### next\_individual

```
 Title   : next_individual
 Usage   : my $ind = $popgenio->next_individual;
 Function: Retrieve the next individual from a dataset
 Returns : Bio::PopGen::IndividualI object
 Args    : none
```

### next\_population

```
 Title   : next_population
 Usage   : my $ind = $popgenio->next_population;
 Function: Retrieve the next population from a dataset
 Returns : Bio::PopGen::PopulationI object
 Args    : none
 Note    : Many implementation will not implement this
```

### write\_individual

```
 Title   : write_individual
 Usage   : $popgenio->write_individual($ind);
 Function: Write an individual out in the file format
 Returns : none
 Args    : L<Bio::PopGen::PopulationI> object(s)
```

### write\_population

```
 Title   : write_population
 Usage   : $popgenio->write_population($pop);
 Function: Write a population out in the file format
 Returns : none
 Args    : L<Bio::PopGen::PopulationI> object(s)
 Note    : Many implementation will not implement this
```