| Bio::PopGen::IO::phase(3pm) | User Contributed Perl Documentation | Bio::PopGen::IO::phase(3pm) |
Bio::PopGen::IO::phase - A parser for Phase format data
# Do not use directly, use through the Bio::PopGen::IO driver
use Bio::PopGen::IO;
my $io = Bio::PopGen::IO->new(-format => 'phase',
-file => 'data.phase');
# 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 phase data.
PHASE is defined in http://www.stat.washington.edu/stephens/instruct2.1.pdf
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
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:
https://github.com/bioperl/bioperl-live/issues
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,
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
| 2018-10-27 | perl v5.26.2 |