Bio::PopGen::IO::prettybase(3) Extract individual allele data from PrettyBase format


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


This object will parse comma delimited PrettyBase output. PrettyBase is defined by the SeattleSNPs

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


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AUTHOR - Jason Stajich



Matthew Hahn,


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


 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)


 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)


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


 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


 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)


 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