Provided by: libbio-perl-perl_1.6.901-2_all bug


       Bio::PopGen::IO::csv -Extract individual allele data from a CSV parser


       #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;


       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


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AUTHOR - Jason Stajich



       Matthew Hahn,


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

        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,

        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)

        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

        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

        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)

        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