Bio::PopGen::IO::phase - A parser for Phase format data

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::PopGen::IO::phase - A parser for Phase format data

SYNOPSIS

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# Do not use directly, use through the Bio::PopGen::IO driver

  use Bio::PopGen::IO;
  my $io = Bio::PopGen::IO->new(-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

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A driver module for Bio::PopGen::IO for parsing phase data.

PHASE is defined in http://www.stat.washington.edu/stephens/instruct2.1.pdf

FEEDBACK

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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

Support

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 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:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Rich Dobson

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Email r.j.dobson-at-qmul.ac.uk

CONTRIBUTORS

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Jason Stajich, jason-at-bioperl.org

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $obj = Bio::PopGen::IO::hapmap->new();
 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,

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 
           'no_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 : L<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 : L<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
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::PopGen::IO::phase
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Rich Dobson <r.j.dobson-at-qmul.ac.uk>
#
# Copyright Rich Dobson
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::PopGen::IO::phase;
use vars qw($FieldDelim $AlleleDelim $NoHeader);
use strict;

($FieldDelim,$AlleleDelim,$NoHeader) =( ',', '\s+',0);




use Bio::PopGen::Individual;
use Bio::PopGen::Population;
use Bio::PopGen::Genotype;

use base qw(Bio::PopGen::IO);



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;

}


sub flag  {

    my $self = shift;
    my $fieldname = shift;
    return unless defined $fieldname;

    return $self->{'_flag'}->{$fieldname} = shift if @_;
    return $self->{'_flag'}->{$fieldname};

}


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


sub next_population{
    my ($self) = @_;
    my @inds;
    while( my $ind = $self->next_individual ) {
	push @inds, $ind;
    }
    Bio::PopGen::Population->new(-individuals => \@inds);
}



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");
    }
}



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");
	} 
    }
}

1;