diff --git a/misc-scripts/xref_mapping/XrefMapper/leishmania_major.pm b/misc-scripts/xref_mapping/XrefMapper/leishmania_major.pm new file mode 100644 index 0000000000000000000000000000000000000000..6c150dd594603495d8c0a2ecf8c2d83c2896a556 --- /dev/null +++ b/misc-scripts/xref_mapping/XrefMapper/leishmania_major.pm @@ -0,0 +1,42 @@ +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; diff --git a/misc-scripts/xref_mapping/XrefMapper/pythium_ultimum.pm b/misc-scripts/xref_mapping/XrefMapper/pythium_ultimum.pm new file mode 100644 index 0000000000000000000000000000000000000000..239e430cba82fed8707b16d528465674640b309c --- /dev/null +++ b/misc-scripts/xref_mapping/XrefMapper/pythium_ultimum.pm @@ -0,0 +1,42 @@ +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;