#
# BioPerl module for Bio::PopGen::IO::csv
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# 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::csv -Extract individual allele data from a CSV parser
=head1 SYNOPSIS
#Do not use directly, use through the Bio::PopGen::IO driver
use Bio::PopGen::IO;
my $io = Bio::PopGen::IO->new(-format => 'csv',
-file => 'data.csv');
# Some IO might support reading in a population at a time
my @population;
while( my $ind = $io->next_individual ) {
push @population, $ind;
}
=head1 DESCRIPTION
This object will parse comma delimited format (CSV) or whatever
delimiter you specify. It currently doesn't handle the more complex
quote escaped CSV format. There are 3 initialization parameters,
the delimiter (-field_delimiter) [default ','], (-allele_delimiter)
[default ' ']. The third initialization parameter is a boolean
-no_header which specifies if there is no header line to read in. All lines starting with '#' will be skipped
When no_header is not specific the data is assumed to be of the following form.
Having a header line this
SAMPLE,MARKERNAME1,MARKERNAME2,...
and each data line having the form (diploid data)
SAMP1,101 102,100 90,a b
or for haploid data
SAMP1,101,100,a
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 CONTRIBUTORS
Matthew Hahn, matthew.hahn-at-duke.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::PopGen::IO::csv;
use vars qw($FieldDelim $AlleleDelim $NoHeader);
use strict;
($FieldDelim,$AlleleDelim,$NoHeader) =( ',', '\s+',0);
# Object preamble - inherits from Bio::Root::Root
use Bio::PopGen::Individual;
use Bio::PopGen::Population;
use Bio::PopGen::Genotype;
use base qw(Bio::PopGen::IO);
=head2 new
Title : new
Usage : my $obj = Bio::PopGen::IO::csv->new();
Function: Builds a new Bio::PopGen::IO::csv object
Returns : an instance of Bio::PopGen::IO::csv
Args : [optional, these are the current defaults]
-field_delimiter => ','
-allele_delimiter=> '\s+'
-no_header => 0,
=cut
sub _initialize {
my($self, @args) = @_;
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;
}
=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};
}
=head2 next_individual
Title : next_individual
Usage : my $ind = $popgenio->next_individual;
Function: Retrieve the next individual from a dataset
Returns : L<Bio::PopGen::IndividualI> object
Args : none
=cut
sub next_individual{
my ($self) = @_;
while( defined( $_ = $self->_readline) ) {
next if( /^\s*\#/ || /^\s+$/ || ! length($_) );
last;
}
return if ! defined $_;
if( $self->flag('no_header') ||
defined $self->{'_header'} ) {
#########new (allows field delim to be the same as the allele delim
my ($samp,@marker_results);
if($self->flag('field_delimiter') ne $self->flag('allele_delimiter')){
($samp,@marker_results) = split($self->flag('field_delimiter'),$_);
}
else{
my $fielddelim = $self->flag('field_delimiter');
my $alleledelim = $self->flag('allele_delimiter');
($samp) = /(^.+?)$fielddelim/;
s/^.+?$fielddelim//;
(@marker_results) = /([\d|\w]+$alleledelim[\d|\w]+)/g;
}
#########end new
my $i = 1;
foreach my $m ( @marker_results ) {
$m =~ s/^\s+//;
$m =~ s/\s+$//;
my $markername;
if( defined $self->{'_header'} ) {
$markername = $self->{'_header'}->[$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=> $samp);
$i++;
}
return Bio::PopGen::Individual->new(-unique_id => $samp,
-genotypes => \@marker_results);
} else {
chomp;
$self->{'_header'} = [split($self->flag('field_delimiter'),$_)];
return $self->next_individual; # rerun loop again
}
return;
}
=head2 next_population
Title : next_population
Usage : my $ind = $popgenio->next_population;
Function: Retrieve the next population from a dataset
Returns : L<Bio::PopGen::PopulationI> object
Args : none
Note : Many implementation will not implement this
=cut
# Plan is to just return the whole dataset as a single population by
# default I think - people would then have each population in a separate
# file.
sub next_population{
my ($self) = @_;
my @inds;
while( my $ind = $self->next_individual ) {
push @inds, $ind;
}
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
Returns : none
Args : L<Bio::PopGen::PopulationI> object(s)
=cut
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, ('SAMPLE', @marker_names)), "\n");
$self->flag('header_written',1);
}
$self->_print( join($fielddelim, $ind->unique_id,
# we're chaining map here, pay attention and read
# starting with the last map
# we'll turn genotypes into allele pairs
# which will be separated by the allele delimiter
map { join($alleledelim,$_->get_Alleles) }
# marker names will be sorted so we don't
# have to worry about this between individuals
# unless the individual set you pass in has
# a mixed set of markers...
# this will turn marker names into Genotypes
map {$ind->get_Genotypes(-marker => $_)}
@marker_names), "\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<Bio::PopGen::PopulationI> object(s)
Note : Many implementation will not implement this
=cut
sub write_population{
my ($self,@pops) = @_;
my $fielddelim = $self->flag('field_delimiter');
# my $alleledelim= $self->flag('allele_delimiter');
my $alleledelim = ' ';
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, ('SAMPLE', @marker_names)),
"\n");
$self->flag('header_written',1);
}
foreach my $ind ( $pop->get_Individuals ) {
$self->_print( join($fielddelim, $ind->unique_id,
# we're chaining map here, pay attention
# and read starting with the last map
# we'll turn genotypes into allele pairs
# which will be separated by the allele
# delimiter
map { join($alleledelim,$_->get_Alleles) }
# marker names will be sorted so we don't
# have to worry about this between individuals
# unless the individual set you pass in has
# a mixed set of markers...
# this will turn marker names into Genotypes
map {$ind->get_Genotypes(-marker => $_)}
@marker_names), "\n");
}
}
}
1;