Bio::PopGen::IO::hapmap - A parser for HapMap output data
# 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;
}
A driver module for Bio::PopGen::IO for parsing hapmap data.
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Email r.j.dobson-at-qmul.ac.uk
Jason Stajich, jason-at-bioperl.org
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::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
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 : A Bio::PopGen::IndividualI object Args : none
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
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)
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
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)
