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.\" ========================================================================
.\"
.IX Title "Bio::PopGen::IO::prettybase 3pm"
.TH Bio::PopGen::IO::prettybase 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::PopGen::IO::prettybase \- Extract individual allele data from PrettyBase format
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Do not use directly, use through the Bio::PopGen::IO driver
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object will parse comma delimited PrettyBase output.  PrettyBase
is defined by the SeattleSNPs http://pga.gs.washington.edu/
.PP
This is expected to be tab delimited (you can vary with the
field_delimiter flag \s-1SITE SAMPLE ALLELE1 ALLELE2\s0
.PP
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
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason\-at\-bioperl.org
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Matthew Hahn, matthew.hahn\-at\-duke.edu
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 11
\& 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 /\et/ ) 
\&           \-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 \*(AqI\*(Aq meaning insert state, and alleles which are
\&                                    \*(Aq\-\*(Aq to a delete state.
\&                                    (default is false)
.Ve
.SS "flag"
.IX Subsection "flag"
.Vb 7
\& 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 
\&           \*(Aqheader\*(Aq, \*(Aqfield_delimiter\*(Aq, or \*(Aqallele_delimiter\*(Aq 
\&           on set, new value (a boolean or undef, optional)
.Ve
.SS "next_individual"
.IX Subsection "next_individual"
.Vb 5
\& Title   : next_individual
\& Usage   : my $ind = $popgenio\->next_individual;
\& Function: Retrieve the next individual from a dataset
\& Returns : Bio::PopGen::IndividualI object
\& Args    : none
.Ve
.SS "next_population"
.IX Subsection "next_population"
.Vb 6
\& 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
.Ve
.SS "write_individual"
.IX Subsection "write_individual"
.Vb 5
\& 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)
.Ve
.SS "write_population"
.IX Subsection "write_population"
.Vb 6
\& 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
.Ve