# $Id: prettybase.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::PopGen::IO::prettybase # # Please direct questions and support issues to # # Cared for by Jason Stajich # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::PopGen::IO::prettybase - Extract individual allele data from PrettyBase format =head1 SYNOPSIS Do not use directly, use through the Bio::PopGen::IO driver =head1 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 =head1 FEEDBACK =head2 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 =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 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.open-bio.org/ =head1 AUTHOR - Jason Stajich Email jason-at-bioperl.org =head1 CONTRIBUTORS Matthew Hahn, matthew.hahn-at-duke.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::PopGen::IO::prettybase; use vars qw($FieldDelim $Header); use strict; ($FieldDelim,$Header) =( '\t',0); use Bio::PopGen::Individual; use Bio::PopGen::Population; use Bio::PopGen::Genotype; use base qw(Bio::PopGen::IO); =head2 new Title : new Usage : my $obj = Bio::PopGen::IO::prettybase->new(); Function: Builds a new Bio::PopGen::IO::prettybase object Returns : an instance of Bio::PopGen::IO::prettybase Args : -field_delimiter => a field delimiter character or regexp (default is /\t/ ) -header => boolean if the file will have a header and parser should skip first line in the file (default is false) -convert_indel_states => convert alleles which are longer than one character to an 'I' meaning insert state, and alleles which are '-' to a delete state. (default is false) =cut sub _initialize { my($self, @args) = @_; my ($fieldsep, $conv_indels, $header) = $self->_rearrange([qw(FIELD_DELIMITER CONVERT_INDEL_STATES HEADER)],@args); $self->flag('header', defined $header ? $header : $Header); $self->flag('field_delimiter',defined $fieldsep ? $fieldsep : $FieldDelim); $self->{'_header'} = undef; $self->{'_parsed_individiuals'} = []; $self->{'_parsed'} = 0; $self->flag('convert_indel',$conv_indels || 0); return 1; } =head2 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) =cut sub flag{ my $self = shift; my $fieldname = shift; return unless defined $fieldname; return $self->{'_flag'}->{$fieldname} = shift if @_; return $self->{'_flag'}->{$fieldname}; } =head2 next_individual Title : next_individual Usage : my $ind = $popgenio->next_individual; Function: Retrieve the next individual from a dataset Returns : Bio::PopGen::IndividualI object Args : none =cut sub next_individual { my ($self) = @_; unless( $self->{'_parsed'} ) { $self->_parse_prettybase; } return $self->{'_parsed_individiuals'}->[$self->{'_iterator'}++]; } =head2 next_population Title : next_population Usage : my $ind = $popgenio->next_population; Function: Retrieve the next population from a dataset Returns : Bio::PopGen::PopulationI object Args : none Note : Many implementation will not implement this =cut # Plan is to just return the whole dataset as a single population by # default I think - people would then have each population in a separate # file. sub next_population{ my ($self) = @_; my @inds; while( my $ind = $self->next_individual ) { push @inds, $ind; } return unless @inds; Bio::PopGen::Population->new(-individuals => \@inds); } sub _parse_prettybase { my $self = shift; my %inds; my $convert_indels = $self->flag('convert_indel'); while( defined( $_ = $self->_readline) ) { next if( /^\s*\#/ || /^\s+$/ || ! length($_) ); my ($site,$sample,@alleles) = split($self->flag('field_delimiter'),$_); if( ! defined $sample ) { warn("sample id is undefined for $_"); next; } for my $allele ( @alleles ) { $allele =~ s/^\s+//; $allele =~ s/\s+$//; if( $convert_indels ) { if( length($allele) > 1 ) { # we have an insert state $allele = 'I'; } elsif( $allele eq '-' ) { # have a delete state $allele = 'D'; } } } my $g = Bio::PopGen::Genotype->new(-alleles => \@alleles, -marker_name => $site, -individual_id=> $sample); if( ! defined $inds{$sample} ) { $inds{$sample} = Bio::PopGen::Individual->new(-unique_id => $sample); } $inds{$sample}->add_Genotype($g); } $self->{'_parsed_individiuals'} = [ values %inds ]; $self->{'_parsed'} = 1; return; } =head2 write_individual Title : write_individual Usage : $popgenio->write_individual($ind); Function: Write an individual out in the file format Returns : none Args : L object(s) =cut sub write_individual{ my ($self,@inds) = @_; foreach my $ind ( @inds ) { if (! ref($ind) || ! $ind->isa('Bio::PopGen::IndividualI') ) { $self->warn("Cannot write an object that is not a Bio::PopGen::IndividualI object"); next; } foreach my $marker ( $ind->get_marker_names ) { my $g = $ind->get_Genotypes(-marker=> $marker); next unless defined $g; $self->_print( join("\t", $marker, $ind->unique_id, $g->get_Alleles), "\n"); } } } =head2 write_population Title : write_population Usage : $popgenio->write_population($pop); Function: Write a population out in the file format Returns : none Args : L object(s) Note : Many implementation will not implement this =cut sub write_population{ my ($self,@pops) = @_; foreach my $pop ( @pops ) { if (! ref($pop) || ! $pop->isa('Bio::PopGen::PopulationI') ) { $self->warn("Cannot write an object that is not a Bio::PopGen::PopulationI object"); next; } my @mnames = $pop->get_marker_names; foreach my $ind ( $pop->get_Individuals ) { if (! ref($ind) || ! $ind->isa('Bio::PopGen::IndividualI') ) { $self->warn("Cannot write an object that is not a Bio::PopGen::IndividualI object"); next; } foreach my $marker ( @mnames ) { my $g = $ind->get_Genotypes(-marker=> $marker); next unless defined $g; $self->_print( join("\t", $marker, $ind->unique_id, $g->get_Alleles), "\n"); } } } } 1;