# BioMirror/Ensembl.pm

=head1 NAME

BioMirror::Ensembl -- BioMirror::Data packages for SwissProt/ExPASY databanks

=cut

package BioMirror::Ensembl;
 @ISA = qw( BioMirror::Data ); 

sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'ENSEMBL',
		name => 'Ensembl Human',
		makeflags => 0, ##$BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		mirror_dir =>	'$zpath/ensembl/current_human/',
		expanded_dir =>	'$dpath/ensembl/current_human/',

		dosummary => 1, 
   	source => {
   		home => 'EnsEMBL',
   		comment => 'Automatic annotation on eukaryotic genomes',
   		url => 'ftp://ftp.ensembl.org/pub/current_human/',
   		web => 'http://www.ensembl.org/',
     	exclude_patt => '^old|flatfiles/genbank',
		  recursive => 'true',
		  compress_prog => 'gzip',
			},

# 		data => [
# 			## ? need data_pat => or such for data file regex patterns ?
# 			'data/flatfiles/embl/',
# 			],

# 		docs => [ ## don't confuse w/ seq data - do we need these unexpanded?
# 			'relnotes.txt',
# 			],

		@_ );
	return $self;
}


# sub getRelease {
# 	my $self= shift;
# 	my $rel= undef;
# 	my $df= BioMirror::replaceVars( $self->expanded_dir . 'relnotes.txt');
# 	my $buf= $self->readChunk($df);
# 	if ($buf =~ m/SWISS-PROT RELEASE ([0-9\.]+)/) {
# 		$rel= "$1";
# 		}
# 	return $rel;
# }


#-------------

package BioMirror::EnsemblFly;
 @ISA = qw( BioMirror::Ensembl ); 

sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'ENSEMBLfly',
		name => 'Ensembl Fly',
		makeflags => 0, ##$BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		mirror_dir =>	'$zpath/ensembl/current_fly',
		expanded_dir =>	'$dpath/ensembl/current_fly',

		dosummary => 0, 
   	source => {
   		home => 'EnsEMBL',
   		comment => 'automatic annotation on eukaryotic genomes',
   		url => 'ftp://ftp.ensembl.org/pub/current_fly/',
   		web => 'http://www.ensembl.org/',
     	exclude_patt => '^old|flatfiles/genbank',
		  recursive => 'true',
		  compress_prog => 'gzip',
			},

		@_ );
	return $self;
}

package BioMirror::EnsemblFugu;
 @ISA = qw( BioMirror::Ensembl ); 

sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'ENSEMBLfugu',
		name => 'Ensembl Fugu',
		makeflags => 0, ##$BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		mirror_dir =>	'$zpath/ensembl/current_fugu',
		expanded_dir =>	'$dpath/ensembl/current_fugu',

		dosummary => 0, 
   	source => {
   		home => 'EnsEMBL',
   		comment => 'automatic annotation on eukaryotic genomes',
   		url => 'ftp://ftp.ensembl.org/pub/current_fugu/',
   		web => 'http://www.ensembl.org/',
     	exclude_patt => '^old|flatfiles/genbank',
		  recursive => 'true',
		  compress_prog => 'gzip',
			},

		@_ );
	return $self;
}


package BioMirror::EnsemblMosquito;
 @ISA = qw( BioMirror::Ensembl ); 

sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'ENSEMBLmosquito',
		name => 'Ensembl Mosquito',
		makeflags => 0, ##$BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		mirror_dir =>	'$zpath/ensembl/current_mosquito',
		expanded_dir =>	'$dpath/ensembl/current_mosquito',

		dosummary => 0, 
   	source => {
   		home => 'EnsEMBL',
   		comment => 'automatic annotation on eukaryotic genomes',
   		url => 'ftp://ftp.ensembl.org/pub/current_mosquito/',
   		web => 'http://www.ensembl.org/',
     	exclude_patt => '^old|flatfiles/genbank',
		  recursive => 'true',
		  compress_prog => 'gzip',
			},

		@_ );
	return $self;
}


package BioMirror::EnsemblMouse;
 @ISA = qw( BioMirror::Ensembl ); 

sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'ENSEMBLmouse',
		name => 'Ensembl Mouse',
		makeflags => 0, ##$BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		mirror_dir =>	'$zpath/ensembl/current_mouse',
		expanded_dir =>	'$dpath/ensembl/current_mouse',

		dosummary => 0, 
   	source => {
   		home => 'EnsEMBL',
   		comment => 'automatic annotation on eukaryotic genomes',
   		url => 'ftp://ftp.ensembl.org/pub/current_mouse/',
   		web => 'http://www.ensembl.org/',
     	exclude_patt => '^old|flatfiles/genbank',
		  recursive => 'true',
		  compress_prog => 'gzip',
			},

		@_ );
	return $self;
}

package BioMirror::EnsemblZebrafish;
 @ISA = qw( BioMirror::Ensembl ); 

sub new {
	my $class= shift;
	my $self = $class->SUPER::new( 
		srsdb => 'ENSEMBLzebrafish',
		name => 'Ensembl Zebrafish',
		makeflags => 0, ##$BioMirror::Data::kFromArchive|$BioMirror::Data::kDoSrsIndex,

		mirror_dir =>	'$zpath/ensembl/current_zebrafish',
		expanded_dir =>	'$dpath/ensembl/current_zebrafish',

		dosummary => 0, 
   	source => {
   		home => 'EnsEMBL',
   		comment => 'automatic annotation on eukaryotic genomes',
   		url => 'ftp://ftp.ensembl.org/pub/current_zebrafish/',
   		web => 'http://www.ensembl.org/',
     	exclude_patt => '^old|flatfiles/genbank',
		  recursive => 'true',
		  compress_prog => 'gzip',
			},

		@_ );
	return $self;
}

## added mar03


package BioMirror::EnsemblRat;
 @ISA = qw( BioMirror::Ensembl );

sub new {
  my $class= shift;
  my $self = $class->SUPER::new(
    srsdb => 'ENSEMBLrat',
    name => 'Ensembl Rat',
    makeflags => 0,  
    mirror_dir =>   '$zpath/ensembl/current_rat',
    expanded_dir => '$dpath/ensembl/current_rat',
  
    dosummary => 0,
  source => {
    home => 'EnsEMBL',
    comment => 'automatic annotation on eukaryotic genomes',
    url => 'ftp://ftp.ensembl.org/pub/current_rat/',
    web => 'http://www.ensembl.org/',
    exclude_patt => '^old|flatfiles/genbank',
    recursive => 'true',
    compress_prog => 'gzip',
    },

   @_ );
  return $self;
}

package BioMirror::EnsemblCelegans;
 @ISA = qw( BioMirror::Ensembl );

sub new {
  my $class= shift;
  my $self = $class->SUPER::new(
    srsdb => 'ENSEMBLcelegans',
    name => 'Ensembl C.elegans',
    makeflags => 0,  
    mirror_dir =>   '$zpath/ensembl/current_celegans',
    expanded_dir => '$dpath/ensembl/current_celegans',
  
    dosummary => 0,
  source => {
    home => 'EnsEMBL',
    comment => 'automatic annotation on eukaryotic genomes',
    url => 'ftp://ftp.ensembl.org/pub/current_celegans/',
    web => 'http://www.ensembl.org/',
    exclude_patt => '^old|flatfiles/genbank',
    recursive => 'true',
    compress_prog => 'gzip',
    },

   @_ );
  return $self;
}


package BioMirror::EnsemblCbriggsae;
 @ISA = qw( BioMirror::Ensembl );

sub new {
  my $class= shift;
  my $self = $class->SUPER::new(
    srsdb => 'ENSEMBLcbriggsae',
    name => 'Ensembl Cbriggsae',
    makeflags => 0,  
    mirror_dir =>   '$zpath/ensembl/current_cbriggsae',
    expanded_dir => '$dpath/ensembl/current_cbriggsae',
  
    dosummary => 0,
  source => {
    home => 'EnsEMBL',
    comment => 'automatic annotation on eukaryotic genomes',
    url => 'ftp://ftp.ensembl.org/pub/current_cbriggsae/',
    web => 'http://www.ensembl.org/',
    exclude_patt => '^old|flatfiles/genbank',
    recursive => 'true',
    compress_prog => 'gzip',
    },

   @_ );
  return $self;
}

package BioMirror::EnsemblMultispecies;
 @ISA = qw( BioMirror::Ensembl );

sub new {
  my $class= shift;
  my $self = $class->SUPER::new(
    srsdb => 'ENSEMBLmultispecies',
    name => 'Ensembl multispecies',
    makeflags => 0,
    mirror_dir =>   '$zpath/ensembl/current_multispecies',
    expanded_dir => '$dpath/ensembl/current_multispecies',
 
    dosummary => 0,
  source => {
    home => 'EnsEMBL',
    comment => 'automatic annotation on eukaryotic genomes',
    url => 'ftp://ftp.ensembl.org/pub/current_multispecies/',
    web => 'http://www.ensembl.org/',
    exclude_patt => '^old|flatfiles/genbank',
    recursive => 'true',
    compress_prog => 'gzip',
    },

   @_ );
  return $self;
}

package BioMirror::EnsemblMart;
 @ISA = qw( BioMirror::Ensembl );

sub new {
  my $class= shift;
  my $self = $class->SUPER::new(
    srsdb => 'ENSEMBLmart',
    name => 'Ensembl Mart',
    makeflags => 0,
    mirror_dir =>   '$zpath/ensembl/current_mart',
    expanded_dir => '$dpath/ensembl/current_mart',
 
    dosummary => 0,
  source => {
    home => 'EnsEMBL',
    comment => 'automatic annotation on eukaryotic genomes',
    url => 'ftp://ftp.ensembl.org/pub/current_mart/',
    web => 'http://www.ensembl.org/',
    exclude_patt => '^old|flatfiles/genbank',
    recursive => 'true',
    compress_prog => 'gzip',
    },

   @_ );
  return $self;
}

#----------------
1;

__END__

oat.% ls $a/ensembl
current_cbriggsae/     current_human/         current_multispecies/
current_celegans/      current_mart/          current_rat/
current_fly/           current_mosquito/      current_zebrafish/
current_fugu/          current_mouse/

touch  -t 0205010000 current_fly/
touch  -t 0211191022 current_fugu/
touch  -t 0211190951 current_human/
touch  -t 0212021444 current_mosquito/
touch  -t 0211191008 current_mouse/
touch  -t 0211191020 current_zebrafish/

touch  -t 0205010000 current_fly/data
touch  -t 0211191022 current_fugu/data
touch  -t 0211190951 current_human/data
touch  -t 0212021444 current_mosquito/data
touch  -t 0211191008 current_mouse/data
touch  -t 0211191020 current_zebrafish/data



current_fly/May  1  2002 data
current_fugu/Nov 19 10:22 data
current_human/Nov 19 09:51 data
current_mosquito/Dec  2 14:44 data
current_mouse/Nov 19 10:08 data
current_zebrafish/Nov 19 10:20 data