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://github.com/bioperl/bioperl-live/issues
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 :
Title : format
Usage : $format = $stream->format()
Function: Get the PopGen format
Returns : PopGen format
Args : none
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
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
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 :
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :