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# $Id$
# BioPerl module for Bio::Pedigree::PedIO
# Please direct questions and support issues to <>
# Cared for by Jason Stajich <>
# Copyright Jason Stajich
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Pedigree::PedIO - PedIO interface
use Bio::Pedigree::PedIO;
my $pedio = new Bio::Pedigree::PedIO(-format => 'genethon');
This is the interface description for the PedIO system. Various
subclasses implement this module and handle reading and writing
pedigrees in specific formats.
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated. - General discussion - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
=head1 AUTHOR - Jason Stajich
Describe contact details here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
# Let the code begin...
package Bio::Pedigree::PedIO;
use strict;
use Bio::Root::Root;
use Bio::Root::IO;
require Exporter;
@ISA = qw(Bio::Root::Root Exporter);
@EXPORT = qw(_digitstr);
=head2 new
Title : new
Usage : do not use this module directly it is an interface
Function: initializes a PedIO object, constructor for shared
data initialization.
IO is initialized in the read/write methods since
a single stream can really only support one pedigree
at a time.
Returns : new Bio::Pedigree::PedIO object
Args :
sub new {
my($class,@args) = @_;
if( $class =~ /Bio::Pedigree::PedIO::(\S+)/ ) {
my ($self) = $class->SUPER::new(@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] ) ||
$format = "\L$format"; # normalize capitalization to lower case
# normalize capitalization
return undef unless( $class->_load_format_module($format) );
return "Bio::Pedigree::PedIO::$format"->new(@args);
# _initialize is chained for all PedIO classes
sub _initialize {
my($self, @args) = @_;
# not really necessary unless we put more in RootI
=head2 read_pedigree
Title : read_pedigree
Usage : my $pedigree = $pedio->read_pedigree(-pedfile => $pedfile,
-datfile => $datfile);
Function: Instatiates a Bio::Pedigree::Pedigree object from a data source
Returns : Bio::Pedigree::Pedigree object or undef on failed reading
Args : -pedfile => pedigree input location
-datfile => (if needed) marker data input location
pedfile/datfile can be filenames or an input stream (GLOB)
sub read_pedigree {
my $self = shift;
$self->throw("Do not call read_pedigree directly from the base PedIO object - the author of ".ref($self). " did not implement read_pedigree method");
=head2 write_pedigree
Title : write_pedigree
Usage : $pedio->write_pedigree( -pedigree => $pedobj,
-pedfile => ">pedfile.ped",
-datfile => ">datfile.dat");
Function: Writes a pedigree to a file or filehandle
as specified by the implementing class
(some formats have the pedigree and marker data
stored in the same file rather than in 2 separate files)
Returns : boolean of success, may throw exception on fatal error
Args : -pedigree => Bio::Pedigree::Pedigree object
-pedfile => pedigree output location
-datfile => (if needed) marker data output location
pedfile/datfile can be filenames or an output stream (GLOB)
sub write_pedigree {
my $self = shift;
$self->throw("Do not call read_pedigree directly from the base PedIO object - the author of ".ref($self). " did not implement read_pedigree method");
=head2 close
Title : close
Usage : $pedio->close();
Function: close all open filehandles and streams
opened by this object
Returns : NONE
Args : NONE
sub close {
my($self) = @_;
if( defined $self->_pedfh ) {
if( defined $self->_datfh ) {
=head2 _initialize_fh
Title : _initialize_fh
Usage : $pedio->_initialize_fh(@args)
Function: Initialize pedigree data input from file or fh
Returns : whether or not a pedfh was initialized
Args : -pedfile -- either filehandle, GLOB, or filename
sub _initialize_fh {
my ($self,@args) = @_;
my ($pedfile,$datfile) = $self->_rearrange([qw(PEDFILE DATFILE)], @args);
my $inited = 0;
if( $pedfile ) {
my $type = ref($pedfile) =~ /GLOB/i ? '-fh' : '-file';
my $fh = new Bio::Root::IO($type => $pedfile);
if( $fh ) {
if( $datfile ) {
my $type = ref($datfile) =~ /GLOB/i ? '-fh' : '-file';
my $fh = new Bio::Root::IO($type => $datfile);
if( $fh ) {
return $inited;
=head2 _pedfh
Title : _pedfh
Usage : $obj->_pedfh($newval)
Returns : Bio::Root::IO
Args : newvalue (optional)
sub _pedfh {
my $obj = shift;
$obj->{'_pedfh'} = shift if @_;
return $obj->{'_pedfh'};
=head2 _datfh
Title : _datfh
Usage : $obj->_datfh($newval)
Returns : Bio::Root::IO object
Args : newvalue (optional)
sub _datfh {
my $obj = shift;
$obj->{'_datfh'} = shift if @_;
return $obj->{'_datfh'};
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL SeqIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
sub _load_format_module {
my ($self,$format) = @_;
my $module = "Bio::Pedigree::PedIO::" . $format;
my $ok;
eval {
$ok = $self->_load_module($module);
if ( $@ ) {
print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the PedIO system please see the PedIO docs.
This includes ways of checking for formats at compile time, not run time
return $ok;
=head2 _guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Example :
Returns : guessed format of filename (lower case)
Args :
sub _guess_format {
my $class = shift;
return unless $_ = shift;
return 'ped' if /\.(ped|pedfile|pped|pedigree|p)$/i;
return 'genbank' if /\.(lapis|lap)$/i;
return 'xml' if /\.xml$/i;
=head2 DESTROY
Usage : called automatically
Function: free allocated resources
Returns : NONE
Args : NONE
my $self = shift;
=head2 _digitstr
Title : _digitstr
Usage : my $str = &_digitstr($ind);
Function: Get an individual string formatted as a N-digit
string unless it is 0, N is 4 by default
Returns : an N-digit string (string)
Args : number to format
sub _digitstr {
my ($indstr,$N) = @_;
$N = $DEFAULTDIGITLEN unless (defined $N && $N =~ /^\d+$/ );
if( $indstr eq '0' || !defined $indstr || $indstr eq '' ) { $indstr = '0';}
else {
while( length($indstr) < $N) {
# prepend '0' to the string while it is less than 4 digits
$indstr = '0' . $indstr;
return $indstr;
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