Bio::PopGen::IO::prettybase - 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 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

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/MailList.shtml - About the mailing lists

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: http://bugzilla.bioperl.org/ Email jason-at-bioperl.org Matthew Hahn, matthew.hahn-at-duke.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::PopGen::IO::prettybase(); 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