Bio::PopGen::IO prettybase
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Summary
Bio::PopGen::IO::prettybase - Extract individual allele data from PrettyBase format
Package variables
No package variables defined.
Included modules
Bio::PopGen::Genotype
Bio::PopGen::Individual
Bio::PopGen::Population
Inherit
Bio::PopGen::IO
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
Methods
_initialize
No description
Code
flagDescriptionCode
next_individualDescriptionCode
next_populationDescriptionCode
_parse_prettybase
No description
Code
write_individualDescriptionCode
write_populationDescriptionCode
Methods description
flagcode    nextTop
 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_individualcodeprevnextTop
 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_populationcodeprevnextTop
 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_individualcodeprevnextTop
 Title   : write_individual
Usage : $popgenio->write_individual($ind);
Function: Write an individual out in the file format
Returns : none
Args : Bio::PopGen::PopulationI object(s)
write_populationcodeprevnextTop
 Title   : write_population
Usage : $popgenio->write_population($pop);
Function: Write a population out in the file format
Returns : none
Args : Bio::PopGen::PopulationI object(s)
Note : Many implementation will not implement this
Methods code
_initializedescriptionprevnextTop
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;
}
flagdescriptionprevnextTop
sub flag {
    my $self = shift;
    my $fieldname = shift;
    return unless defined $fieldname;
    
    return $self->{'_flag'}->{$fieldname} = shift if @_;
    return $self->{'_flag'}->{$fieldname};
}
next_individualdescriptionprevnextTop
sub next_individual {
    my ($self) = @_;
    unless( $self->{'_parsed'} ) {
	$self->_parse_prettybase;
    }
    return $self->{'_parsed_individiuals'}->[$self->{'_iterator'}++];
}
next_populationdescriptionprevnextTop
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);
}
_parse_prettybasedescriptionprevnextTop
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 ]; $self->{'_parsed'} = 1; return;
}
write_individualdescriptionprevnextTop
sub write_individual {
    my ($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, 
				$g->get_Alleles), "\n");	    
	}
    }
}
write_populationdescriptionprevnextTop
sub write_population {
    my ($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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
CONTRIBUTORSTop
Matthew Hahn, matthew.hahn-at-duke.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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)