adamjohnwright
commented
6 years ago This has been implemented on staging
Closed adamjohnwright closed 6 years ago
adamjohnwright
commented
6 years ago This has been implemented on staging
Note: all of the species tests have (I think) an implicit bug where they will fail to do the right thing when viewing results for the Hawaiian strain (c_elegans_PRJNA275000), assuming there are object pages like that (or when there are, whatever).
Clone qw(GENES CLONES LINKS_AND_SUPERLINKS GENOMIC_CANONICAL)
“Curated_Genes%2CYACs_Fosmids_Cosmids%2CContig%20submissions%2CLinks%20and%20Superlinks”
Cds $self->_parsed_species =~ /elegans/ ? ($self->method->{data}{method} eq 'history') ? [qw(HISTORICAL_GENES)] : [qw(GENES TRANSPOSONS TRANSPOSON_GENES EST_BEST PROTEIN_MOTIFS)] : undef, };
Elegans/History: “Gene%20Models%20(historical)” Elegans/not history: “Curated_Genes%2CTransposon%20Genes%2CTransposons%2CESTs%20(best)%2CProtein%20motifs”
Gene $self->object->Corresponding_transposon ? [qw/TRANSPOSONS TRANSPOSON_GENES/] : [qw/GENES VARIATIONS_CLASSICAL_ALLELES CLONES/]
Corresponding transposon: “Transposons%2CTransposon%20Genes” Else: “Curated_Genes%2CClassical_alleles%2CYACs_Fosmids_Cosmids”
Operon [qw/GENES OPERONS/]
“Curated_Genes%2COperons”
Pcr product qw/GENES MICROARRAY_OLIGO_PROBES PCR_PRODUCTS ORFEOME_PCR_PRODUCTS CLONES/
“Curated_Genes%2CMicroarray%20oligo%20probes%2CPCR%20Assays%2CORFeome%20PCR%20Products%2CYACs_Fosmids_Cosmids”
Protein [qw(GENES PROTEIN_MOTIFS)]
“Curated_Genes%2CProtein%20motifs”
Pseudogene $self->_parsed_species =~ /elegans/ ? [qw(GENES)] : undef,
“Curated_Genes”
Sequence $self->_parsed_species =~ /elegans/ ? [qw(GENES EST_BEST)] : undef
“Curated_Genes%2CESTs%20(best)”
Feature Note: I’ll put in the translations, but this should return empty until we’re ready to implement in the sequence features widget. [qw/GENES RNASEQ_ASYMMETRIES RNASEQ RNASEQ_SPLICE POLYSOMES MICRO_ORF DNASEI_HYPERSENSITIVE_SITE REGULATORY_REGIONS PROMOTER_REGIONS HISTONE_BINDING_SITES TRANSCRIPTION_FACTOR_BINDING_REGION TRANSCRIPTION_FACTOR_BINDING_SITE GENOME_SEQUENCE_ERROR_CORRECTED BINDING_SITES_PREDICTED BINDING_SITES_CURATED BINDING_REGIONS GENOME_SEQUENCE_ERROR/],
“Curated_Genes%2CRNASeq%20Asymmetries%2CRNASeq%2CRNASeq%20introns%2CPolysomes%2CDNAseI%20hypersensitive%20site%2CRegulatory%20regions%2CPromoter%20regions%2CHistone%20binding%20sites%2CTranscription%20factor%20binding%20regions%2CTranscription%20factor%20binding%20sites%2CGenome%20sequence%20corrections%2CBinding%20sites%20(predicted)%2CBinding%20sites%20(curated)%2CBinding%20regions%2CGenome%20sequence%20errors”
Transcript $self->_parsed_species =~ /elegans/ ? [qw(GENES EST_BEST)] : undef
“Curated_Genes%2CESTs%20(best)”
Transposon qw/TRANSPOSON_GENES TRANSPOSONS/
“Transposon%20Genes%2CTransposons”
Variation if ($self->_parsed_species eq 'c_elegans') { @tracks = qw(GENES VARIATIONS_CLASSICAL_ALLELES VARIATIONS_HIGH_THROUGHPUT_ALLELES VARIATIONS_POLYMORPHISMS VARIATIONS_CHANGE_OF_FUNCTION_ALLELES VARIATIONS_CHANGE_OF_FUNCTION_POLYMORPHISMS VARIATIONS_TRANSPOSON_INSERTION_SITES VARIATIONS_MILLION_MUTATION_PROJECT); } elsif ($self->_parsed_species eq 'c_briggsae') { @tracks = qw(GENES VARIATIONS_POLYMORPHISMS); } else { @tracks = qw/GENES/; }
C_elegans: “Curated_Genes%2CClassical_alleles%2CHigh-throughput%20alleles%2CPolymorphisms%2CChange-of-function%20alleles%2CChange-of-function%20polymorphisms%2CTransposon%20insert%20sites%2CMillion%20Mutation%20Project”
C_briggsae: “Curated_Genes%2CPolymorphisms”
Other: “Curated_Genes”