sync w/ main trunk

[bioperl-live.git] / Bio / PopGen / IO / csv.pm

# $Id$
#
# 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:
  
L<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:

  http://bugzilla.open-bio.org/

=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;