| Bio::PopGen::IO::hapmap(3pm) | User Contributed Perl Documentation | Bio::PopGen::IO::hapmap(3pm) |
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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Please direct usage questions or support issues to the mailing list:
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.
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:
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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
See Bio::PopGen::IndividualI
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 Bio::PopGen::PopulationI
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 Bio::PopGen::PopulationI
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 Bio::PopGen::PopulationI
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)
| 2018-10-27 | perl v5.26.2 |