Bio::PopGen::IO(3pm) User Contributed Perl Documentation Bio::PopGen::IO(3pm)
NAME
Bio::PopGen::IO - Input individual,marker,allele information
SYNOPSIS
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;
}
DESCRIPTION
This is a generic interface to reading in population genetic data (of which there really isn't too many standard formats). This
implementation makes it easy to provide your own parser for the data. You need to only implement one function next_individual. You can
also implement next_population if your data has explicit information about population memberhsip for the indidviduals.
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email 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->new();
Function: Builds a new Bio::PopGen::IO object
Returns : an instance of Bio::PopGen::IO
Args :
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 $pop = $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 implementation 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 implementation format
Returns : none
Args : L<Bio::PopGen::PopulationI> object(s)
Note : Many implementation will not implement this
newFh
Title : newFh
Usage : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format')
Function: does a new() followed by an fh()
Example : $fh = Bio::SeqIO->newFh(-file=>$filename,-format=>'Format')
$sequence = <$fh>; # read a sequence object
print $fh $sequence; # write a sequence object
Returns : filehandle tied to the Bio::SeqIO::Fh class
Args :
See Bio::SeqIO::Fh
fh
Title : fh
Usage : $obj->fh
Function:
Example : $fh = $obj->fh; # make a tied filehandle
$sequence = <$fh>; # read a sequence object
print $fh $sequence; # write a sequence object
Returns : filehandle tied to Bio::SeqIO class
Args : none
_load_format_module
Title : _load_format_module
Usage : *INTERNAL Bio::PopGen::IO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
_guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
perl v5.14.2 2012-03-02 Bio::PopGen::IO(3pm)