NAME¶
Bio::PopGen::IO::phase - A parser for Phase format data
SYNOPSIS¶
# 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;
}
DESCRIPTION¶
A driver module for Bio::PopGen::IO for parsing phase data.
PHASE is defined in
http://www.stat.washington.edu/stephens/instruct2.1.pdf
FEEDBACK¶
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
Support¶
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.
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:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Rich Dobson¶
Email r.j.dobson-at-qmul.ac.uk
CONTRIBUTORS¶
Jason Stajich, jason-at-bioperl.org
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
new¶
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,
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)
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
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
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)
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