Bio::PopGen::IO phase
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::PopGen::IO::phase - A parser for Phase format data
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
  use Bio::PopGen::IO;
  my $io = new Bio::PopGen::IO(-format => 'phase',
                               -file   => 'data.phase');

  # Some IO might support reading in a population at a time

  my @population;
  while( my $ind = $io->next_individual ) {
      push @population, $ind;
  }
Description
A driver module for Bio::PopGen::IO for parsing phase data.
PHASE is defined in http://www.stat.washington.edu/stephens/instruct2.1.pdf
Methods
_initialize
No description
Code
flagDescriptionCode
next_individualDescriptionCode
next_populationDescriptionCode
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 
           'no_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) = @_;

    $Bio::PopGen::Genotype::BlankAlleles='';

    my ($fieldsep,$all_sep, 
	$noheader) = $self->_rearrange([qw(FIELD_DELIMITER
					   ALLELE_DELIMITER
					   NO_HEADER)],@args);

    $self->flag('no_header', defined $noheader ? $noheader : $NoHeader);
    $self->flag('field_delimiter',defined $fieldsep ? $fieldsep : $FieldDelim);
    $self->flag('allele_delimiter',defined $all_sep ? $all_sep : $AlleleDelim);

    $self->{'_header'} = undef;
    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) = @_;

    my ($sam,@marker_results,$number_of_ids,$number_of_markers,
	$marker_positions,$micro_snp);

    while( defined( $_ = $self->_readline) ) {
	next if( /^\s+$/ || ! length($_) );
	last;
    }
    
    return unless defined $_; 
    if( $self->flag('no_header') || defined $self->{'_header'} ) {

	####### sometimes there is some marker info at the start of a phase input file
	####### we collect it in the next few lines if there is. Should this info be held in a marker object?

	if(!$self->{'_count'} && /^\s*\d+$/){
	    $self->flag('number_of_ids',$_);
	    #print "number_of_ids : $number_of_ids\n";
	    $self->{'_count'}++;
	    return $self->next_individual;
	} elsif($self->{'_count'} == 1 && /^\s*\d+$/){
	    $self->flag('number_of_markers',$_);
	    #print "number_of_markers : $number_of_markers\n";
	    $self->{'_count'}++;
	    return $self->next_individual;
	} elsif($self->{'_count'} == 2 && /^\s*P\s\d/){
	    $self->flag('marker_positions',$_);
	    #print "marker_position : $marker_positions\n";
	    $self->{'_count'}++;
	    return $self->next_individual;
	} elsif($self->{'_count'} == 3 && /^\s*(M|S)+\s*$/i){
	    $self->flag('micro_snp',$_);
	    #print "microsat or snp : $micro_snp\n";
	    $self->{'_count'}++;
	    return $self->next_individual;
	} elsif(/^\s*\#/){
	    ($self->{'_sam'}) = /^\s*\#(.+)/;
	    #print "sample : $self->{'_sam'}\n";
	    $self->{'_count'}++;
	    return $self->next_individual;
	} else {
	    chomp $_;
	    if( $self->{'_row1'} ) {
		# if we are looking at the 2nd row of alleles for this id

		@{$self->{'_second_row'}} = 
		    split($self->flag('field_delimiter'),$_);

		for my $i(0 .. $#{$self->{'_first_row'}}){

		    push(@{$self->{'_marker_results'}},
			 $self->{'_first_row'}->[$i].
			 $self->flag('field_delimiter').
			 $self->{'_second_row'}->[$i]);
		}
		$self->{'_row1'} = 0;
	    } else {
		# if we are looking at the first row of alleles for this id
		@{$self->{'_marker_results'}} = ();
		@{$self->{'_first_row'}} = split($self->flag('field_delimiter'),$_);
		$self->{'_row1'} = 1;
		return $self->next_individual;
	    }
	}

	my $i = 1;
	foreach my $m ( @{$self->{'_marker_results'}} ) {
	    $m =~ s/^\s+//;
	    $m =~ s/\s+$//;
	    my $markername;
	    if( defined $self->{'_header'} ) {
		$markername = $self->{'_header'}->[$i] || "Marker$i";
	    } else { 
		$markername = "Marker$i";
	    }
	    $self->debug( "markername is $markername alleles are $m\n");
	    my @alleles = split($self->flag('allele_delimiter'), $m);	

	    $m = new Bio::PopGen::Genotype(-alleles      =>\@alleles,
					   -marker_name  => $markername,
					   -individual_id=> $self->{'_sam'}); 
	    $i++; 
	}
	return new Bio::PopGen::Individual(-unique_id => $self->{'_sam'},
					   -genotypes =>\@{$self->{'_marker_results'}},
					   );

    } else {
	chomp;
	$self->{'_header'} = [split($self->flag('field_delimiter'),$_)];
	return $self->next_individual; # rerun loop again
    }
    return;
}
next_populationdescriptionprevnextTop
sub next_population {
    my ($self) = @_;
    my @inds;
    while( my $ind = $self->next_individual ) {
	push @inds, $ind;
    }
    Bio::PopGen::Population->new(-individuals =>\@ inds);
}
write_individualdescriptionprevnextTop
sub write_individual {
    my ($self,@inds) = @_;
    my $fielddelim  = $self->flag('field_delimiter');
    my $alleledelim = $self->flag('allele_delimiter');

    foreach my $ind ( @inds ) {
	if (! ref($ind) || ! $ind->isa('Bio::PopGen::IndividualI') ) {
	    $self->warn("Cannot write an object that is not a Bio::PopGen::IndividualI object ($ind)");
	    next;
	}
	# we'll go ahead and sort these until
	# we have a better way to insure a consistent order
	my @marker_names = sort $ind->get_marker_names;
	if( ! $self->flag('no_header') && 
	    ! $self->flag('header_written') ) {
	    $self->_print(join($fielddelim, ('SAM', @marker_names)), "\n");
	    $self->flag('header_written',1);
	}

	my(@row1,@row2);

	for (@marker_names){
	    my $geno = $ind->get_Genotypes(-marker => $_);
	    my @alleles = $geno->get_Alleles();
	    push(@row1,$alleles[0]);
	    push(@row2,$alleles[1]);
	}
	$self->_print("#",$ind->unique_id,"\n",
		      join($fielddelim,@row1),"\n",
		      join($fielddelim,@row2),"\n");
    }
}
write_populationdescriptionprevnextTop
sub write_population {
    my ($self,@pops) = @_;
    my $fielddelim  = $self->flag('field_delimiter');
    my $alleledelim = $self->flag('allele_delimiter');

    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;
	}
	# we'll go ahead and sort these until
	# we have a better way to insure a consistent order
	my @marker_names = sort $pop->get_marker_names;
	if( ! $self->flag('no_header') && 
	    ! $self->flag('header_written') ) {
	    $self->_print( join($fielddelim, ('SAM', @marker_names)), 
			   "\n");
	    $self->flag('header_written',1);
	}
	foreach my $ind ( $pop->get_Individuals ) {
	    my(@row1,@row2);
	    for (@marker_names){
		my $geno = $ind->get_Genotypes(-marker => $_);
		my @alleles = $geno->get_Alleles();
		push (@row1,$alleles[0]);
		push (@row2,$alleles[1]);
	    }
	    $self->_print("#",$ind->unique_id,"\n",
			  join($fielddelim,@row1),"\n",
			  join($fielddelim,@row2),"\n");
	} 
    }
}
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
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:
  http://bugzilla.open-bio.org/
AUTHOR - Rich DobsonTop
Email r.j.dobson-at-qmul.ac.uk
CONTRIBUTORSTop
Jason Stajich, jason-at-bioperl.org
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 = new Bio::PopGen::IO::hapmap();
 Function: Builds a new Bio::PopGen::IO::hapmap object 
 Returns : an instance of Bio::PopGen::IO::hapmap
 Args    : [optional, these are the current defaults] 
           -field_delimiter => ','
           -allele_delimiter=> '\s+'
           -no_header       => 0,