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Commit 1203da90 authored by Arnaud Kerhornou's avatar Arnaud Kerhornou
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removed as we use now in EnsemblGenomes a generic eukaryota module, which is easier to maintain

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misc-scripts/xref_mapping/XrefMapper/daphnia_pulex.pm deleted 100644 → 0
+ 0
− 42
View file @ be770bee
package XrefMapper::daphnia_pulex;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["daphnia_pulex","*"]]];
}
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
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misc-scripts/xref_mapping/XrefMapper/fusarium_oxysporum.pm deleted 100644 → 0
+ 0
− 42
View file @ be770bee
package XrefMapper::fusarium_oxysporum;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["fusarium_oxysporum","*"]]];
}
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
1;
misc-scripts/xref_mapping/XrefMapper/gibberella_moniliformis.pm deleted 100644 → 0
+ 0
− 42
View file @ be770bee
package XrefMapper::gibberella_moniliformis;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["gibberella_moniliformis","*"]]];
}
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
1;
misc-scripts/xref_mapping/XrefMapper/gibberella_zeae.pm deleted 100644 → 0
+ 0
− 42
View file @ be770bee
package XrefMapper::gibberella_zeae;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["gibberella_zeae","*"]]];
}
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
1;
misc-scripts/xref_mapping/XrefMapper/hyaloperonospora_arabidopsidis.pm deleted 100644 → 0
+ 0
− 42
View file @ be770bee
package XrefMapper::hyaloperonospora_arabidopsidis;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["hyaloperonospora_arabidopsidis","*"]]];
}
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
1;
misc-scripts/xref_mapping/XrefMapper/leishmania_major.pm deleted 100644 → 0
+ 0
− 42
View file @ be770bee
package XrefMapper::leishmania_major;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["leishmania_major","*"]]];
}
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
1;
misc-scripts/xref_mapping/XrefMapper/mycosphaerella_graminicola.pm deleted 100644 → 0
+ 0
− 42
View file @ be770bee
package XrefMapper::mycosphaerella_graminicola;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["mycosphaerella_graminicola","*"]]];
}
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
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misc-scripts/xref_mapping/XrefMapper/nectria_haematococca.pm deleted 100644 → 0
+ 0
− 75
View file @ be770bee
=head1 XrefMapper::nectria_haematococca
Gets created in xref_mapper.pl like this:
my $mapper = XrefMapper::BasicMapper->process_file($file, !$notverbose, $no_xref);
the process_file method returns an instance of a species specific xref mapper like this:
$mapper = "XrefMapper::$module"->new();
=cut
package XrefMapper::nectria_haematococca;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
=head1 get_set_lists
Gets called in XrefMapper::SubmitMapper:
if($self->mapper->can('get_set_lists')){
@lists =@{$self->mapper->get_set_lists()}; }
else {
@lists =@{$self->get_set_lists()};
}
=cut
sub get_set_lists {
return [["ExonerateGappedBest1", ["nectria_haematococca","*"]]];
}
=head1 transcript_display_xref_sources
Gets called in XrefMapper::DisplayXrefs:
if( $self->mapper->can("transcript_display_xref_sources") ){
($presedence, $ignore) = @{$self->mapper->transcript_display_xref_sources(1)}; # FULL update mode pass 1
}
else{
($presedence, $ignore) = @{$self->transcript_display_xref_sources(1)}; # FULL update mode pass 1
}
=cut
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
TRNASCAN_SE
RNAMMER
RFAM
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
1;
misc-scripts/xref_mapping/XrefMapper/puccinia_triticina.pm deleted 100644 → 0
+ 0
− 42
View file @ be770bee
package XrefMapper::puccinia_triticina;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["puccinia_triticina","*"]]];
}
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
1;
misc-scripts/xref_mapping/XrefMapper/pythium_ultimum.pm deleted 100644 → 0
+ 0
− 42
View file @ be770bee
package XrefMapper::pythium_ultimum;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["pythium_ultimum","*"]]];
}
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
1;
misc-scripts/xref_mapping/XrefMapper/ustilago_maydis.pm deleted 100644 → 0
+ 0
− 42
View file @ be770bee
package XrefMapper::ustilago_maydis;
use XrefMapper::BasicMapper;
use vars qw(@ISA);
@ISA = qw(XrefMapper::BasicMapper);
sub get_set_lists {
return [["ExonerateGappedBest1", ["ustilago_maydis","*"]]];
}
sub transcript_display_xref_sources {
my $self = shift;
my $fullmode = shift;
my @list = qw(
Uniprot_genename
);
my %ignore;
# Both methods
if(!$fullmode){
$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
}
else{
$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
}
return [\@list,\%ignore];
}
1;
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