#
# BioPerl module for Bio::PopGen::IO::hapmap
#
# 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
=head1 NAME
Bio::PopGen::IO::hapmap - A parser for HapMap output data
=head1 SYNOPSIS
# Do not use directly, use through the Bio::PopGen::IO driver
use Bio::PopGen::IO;
my $io = Bio::PopGen::IO->new(-format => 'hapmap',
-file => 'data.hapmap');
# Some IO might support reading in a population at a time
my @population;
while( my $ind = $io->next_individual ) {
push @population, $ind;
}
=head1 DESCRIPTION
A driver module for Bio::PopGen::IO for parsing hapmap data.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Rich Dobson
Email r.j.dobson-at-qmul.ac.uk
=head1 CONTRIBUTORS
Jason Stajich, jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::PopGen::IO::hapmap;
use vars qw($FieldDelim $AlleleDelim $NoHeader $StartingCol);
use strict;
($FieldDelim,$AlleleDelim,$NoHeader,$StartingCol) =( '\s+','',0,11);
use Bio::PopGen::Individual;
use Bio::PopGen::Population;
use Bio::PopGen::Genotype;
use base qw(Bio::PopGen::IO);
=head2 new
Title : new
Usage : my $obj = Bio::PopGen::IO::hapmap->new();
Function: Builds a new Bio::PopGen::IO::hapmap object
Returns : an instance of Bio::PopGen::IO::hapmap
Args : [optional, these are the current defaults]
-field_delimiter => ','
-allele_delimiter=> '\s+'
-no_header => 0,
-starting_column => 11
=cut
sub _initialize {
my($self, @args) = @_;
$Bio::PopGen::Genotype::BlankAlleles='';
my ($fieldsep,$all_sep,
$noheader, $start_col) = $self->_rearrange([qw(FIELD_DELIMITER
ALLELE_DELIMITER
NO_HEADER
STARTING_COLUMN)],
@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->starting_column(defined $start_col ? $start_col : $StartingCol );
$self->{'_header'} = undef;
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
'no_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};
}
sub _pivot {
my ($self) = @_;
my (@cols,@rows,@idheader);
while ($_ = $self->_readline){
chomp($_);
next if( /^\s*\#/ || /^\s+$/ || ! length($_) );
if( /^rs\#\s+alleles\s+chrom\s+pos\s+strand/ ) {
@idheader = split $self->flag('field_delimiter');
} else {
push @cols, [split $self->flag('field_delimiter')];
}
}
my $startingcol = $self->starting_column;
$self->{'_header'} = [ map { $_->[0] } @cols];
for my $n ($startingcol.. $#{ $cols[ 0 ]}) {
my $column = [ $idheader[$n],
map{ $_->[ $n ] } @cols ];
push (@rows, $column);
}
$self->{'_pivot'} = [@rows];
$self->{'_i'} = 0;
}
=head2 next_individual
Title : next_individual
Usage : my $ind = $popgenio->next_individual;
Function: Retrieve the next individual from a dataset
Returns : A Bio::PopGen::IndividualI object
Args : none
See L<Bio::PopGen::IndividualI>
=cut
sub next_individual {
my ($self) = @_;
unless($self->{'_pivot'}){
#if it's the first time then pivot the table and store.
#Lines will now be read from the stored pivot version of the input file
$self->_pivot;
}
$_ = $self->{'_pivot'}->[$self->{'_i'}++];
return unless defined $_;
# Store all the marker related info. Now that the pivot has taken
# place this is in the first few lines of the file Maybe this
# should be put in a marker object. Doesn't seem to fit too well
# though
my ($samp,@marker_results) = @$_;
# at some point use all this info
my $i = 1;
foreach my $m ( @marker_results ) {
$m =~ s/^\s+//;
$m =~ s/\s+$//;
my $markername;
if( defined $self->{'_header'} ) {
$markername = $self->{'_header'}->[$i-1];
} else {
$markername = "Marker$i";
}
my @alleles = split($self->flag('allele_delimiter'), $m);
if( @alleles != 2 ) {
$self->warn("$m for $samp\n");
} else {
$m = Bio::PopGen::Genotype->new(-alleles => \@alleles,
-marker_name => $markername,
-individual_id=> $samp);
}
$i++;
}
return new Bio::PopGen::Individual(-unique_id => $samp,
-genotypes => \@marker_results);
}
=head2 next_population
Title : next_population
Usage : my $ind = $popgenio->next_population;
Function: Retrieve the next population from a dataset
Returns : Bio::PopGen::PopulationI object
Args : none
Note : Many implementation will not implement this
See L<Bio::PopGen::PopulationI>
=cut
sub next_population {
my ($self) = @_;
my @inds;
while( my $ind = $self->next_individual ) {
push @inds, $ind;
}
Bio::PopGen::Population->new(-individuals => \@inds);
}
=head2 write_individual
Title : write_individual
Usage : $popgenio->write_individual($ind);
Function: Write an individual out in the file format
NOT SUPPORTED BY hapmap format
Returns : none
Args : Bio::PopGen::PopulationI object(s)
See L<Bio::PopGen::PopulationI>
=cut
sub write_individual {
my ($self,@inds) = @_;
# data from hapmap is output, not input, so
# we don't need a method for writing and input file
$self->throw_not_implemented();
}
=head2 write_population
Title : write_population
Usage : $popgenio->write_population($pop);
Function: Write a population out in the file format
NOT SUPPORTED BY hapmap format
Returns : none
Args : Bio::PopGen::PopulationI object(s)
Note : Many implementation will not implement this
See L<Bio::PopGen::PopulationI>
=cut
sub write_population {
my ($self,@inds) = @_;
$self->throw_not_implemented();
}
=head2 starting_column
Title : starting_column
Usage : $obj->starting_column($newval)
Function: Column where data starts
Example :
Returns : value of starting_column (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub starting_column{
my $self = shift;
return $self->{'starting_column'} = shift if @_;
return $self->{'starting_column'};
}
1;