| Bio::PopGen::IO(3pm) | User Contributed Perl Documentation | Bio::PopGen::IO(3pm) |
Bio::PopGen::IO - Input individual,marker,allele information
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;
}
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.
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 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->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
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 $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
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)
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
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 :
| 2018-10-27 | perl v5.26.2 |