Reference

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

History