Bio::PopGen IO
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Summary
Bio::PopGen::IO - Input individual,marker,allele information
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Inherit
Bio::Root::IO
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.
Methods
newDescriptionCode
_initialize
No description
Code
next_individualDescriptionCode
next_populationDescriptionCode
write_individualDescriptionCode
write_populationDescriptionCode
newFhDescriptionCode
fhDescriptionCode
_load_format_moduleDescriptionCode
_guess_formatDescriptionCode
close
No description
Code
DESTROY
No description
Code
TIEHANDLE
No description
Code
READLINE
No description
Code
PRINT
No description
Code
Methods description
newcode    nextTop
 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_individualcodeprevnextTop
 Title   : next_individual
Usage : my $ind = $popgenio->next_individual;
Function: Retrieve the next individual from a dataset
Returns : Bio::PopGen::IndividualI object
Args : none
next_populationcodeprevnextTop
 Title   : next_population
Usage : my $pop = $popgenio->next_population;
Function: Retrieve the next population from a dataset
Returns : Bio::PopGen::PopulationI object
Args : none
Note : Many implementation will not implement this
write_individualcodeprevnextTop
 Title   : write_individual
Usage : $popgenio->write_individual($ind);
Function: Write an individual out in the implementation format
Returns : none
Args : Bio::PopGen::PopulationI object(s)
write_populationcodeprevnextTop
 Title   : write_population
Usage : $popgenio->write_population($pop);
Function: Write a population out in the implementation format
Returns : none
Args : Bio::PopGen::PopulationI object(s)
Note : Many implementation will not implement this
newFhcodeprevnextTop
 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
fhcodeprevnextTop
 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_modulecodeprevnextTop
 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_formatcodeprevnextTop
 Title   : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  if( $class =~ /Bio::PopGen::IO::(\S+)/ ) {
    my ($self) = $class->SUPER::new(@args);	
    $self->_initialize(@args);
    return $self;
  } else { 
    my %param = @args;
    @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} || $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'csv'; # normalize capitalization to lower case
$format = "\L$format"; return unless( $class->_load_format_module($format) ); return "Bio::PopGen::IO::${format}"->new(@args); }
}
_initializedescriptionprevnextTop
sub _initialize {
    my($self, @args) = @_;
#    my ($indfact, $popfact) = $self->_rearrange([qw(INDIVIDUAL_FACTORY
# POPULATION_FACTORY)],
# @args);
# $indfact = Bio::PopGen::IndividualBuilder->new() unless $indfact;
# $indfact = Bio::PopGen::PopulationBuilder->new() unless $indfact;
# initialize the IO part
$self->_initialize_io(@args); return 1;
}
next_individualdescriptionprevnextTop
sub next_individual {
    my ($self) = @_;
    $self->throw_not_implemented();
}
next_populationdescriptionprevnextTop
sub next_population {
    my ($self) = @_;
    $self->throw_not_implemented();
}
write_individualdescriptionprevnextTop
sub write_individual {
    my ($self) = @_;
    $self->throw_not_implemented();
}
write_populationdescriptionprevnextTop
sub write_population {
    my ($self) = @_;
    $self->throw_not_implemented();
}
newFhdescriptionprevnextTop
sub newFh {
  my $class = shift;
  return unless my $self = $class->new(@_);
  return $self->fh;
}
fhdescriptionprevnextTop
sub fh {
  my $self = shift;
  my $class = ref($self) || $self;
  my $s = Symbol::gensym;
  tie $$s,$class,$self;
  return $s;
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
  my ($self,$format) = @_;
  my $module = "Bio::PopGen::IO::" . $format;
  my $ok;
  
  eval {
      $ok = $self->_load_module($module);
  };
  if ( $@ ) {
      print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the Bio::PopGen::IO system please see the
Bio::PopGen::IO docs. This includes ways of checking for formats at
compile time, not run time
END
; } return $ok;
}
_guess_formatdescriptionprevnextTop
sub _guess_format {
   my $class = shift;
   return unless $_ = shift;
   return 'csv'   if (/csv/i or /\.dat\w$/i);
}
closedescriptionprevnextTop
sub close {
     my $self = shift;
    $self->SUPER::close(@_);
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;
    $self->close();
}
TIEHANDLEdescriptionprevnextTop
sub TIEHANDLE {
  my $class = shift;
  return bless {processor => shift}, $class;
}
READLINEdescriptionprevnextTop
sub READLINE {
  my $self = shift;
  return $self->{'processor'}->next_result() unless wantarray;
  my (@list, $obj);
  push @list, $obj while $obj = $self->{'processor'}->next_result();
  return @list;
}
PRINTdescriptionprevnextTop
sub PRINT {
  my $self = shift;
  $self->{'processor'}->write_result(@_);
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
formatTop
 Title   : format
Usage : $format = $stream->format()
Function: Get the PopGen format
Returns : PopGen format
Args : none