CSC

% cacheebeyesearch -cachefile ~/.embossdata/qatests.server.ebeye -auto 

Generates server cache file for EB-eye search domains
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-cachefile]         outfile    [server.$(servername)] Server cache output
                                  file

   Additional (Optional) qualifiers:
   -outfile            outfile    [stdout] Output file name

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   "-cachefile" associated qualifiers
   -odirectory1        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

# qatests.server.ebeye 2011-07-15 12:00:00

DB toucan [
  method: ebeye
  dbalias: 2can
  fields: "description, domain_source, id, name"
  return: "description, domain_source, id, name"
  format: "text"
  hasaccession: "N"
]

DB arrayexpress_repository [
  method: ebeye
  dbalias: arrayexpress-repository
  fields: "acc, authors, biomaterial-characteristics, description, domain_source, experimentalfactors-factorvalues, id, keywords, name, release_date"
  return: "acc, authors, biomaterial-characteristics, description, domain_source, experimentalfactors-factorvalues, id, keywords, name, release_date"
  format: "text"
  hasaccession: "N"
]

DB astd [
  method: ebeye
  dbalias: astd
  fields: "creation_date, description, exon, id, intron, keywords, last_modification_date, name, nonsense-mediated_decay, polya_site, protein, transcription_start_site, tss_cluster"
  return: "description, exon, id, intron, keywords, last_modification_date, name, nonsense-mediated_decay, polya_site, protein, transcription_start_site, tss_cluster"
  format: "text"
  hasaccession: "N"
]

DB atlas_experiments [
  method: ebeye
  dbalias: atlas-experiments
  fields: "creation_date, description, domain_source, id, last_modification_date, name"
  return: "description, domain_source, id, last_modification_date, name"
  format: "text"
  hasaccession: "N"
]

DB atlas_genes [
  method: ebeye
  dbalias: atlas-genes
  fields: "cell_line, cell_type, cint_jgi_v1, cint_jgi_v2, compound, creation_date, description, developmental_stage, disease, disease_state, domain_source, ensfamily_description, entrezgene, flybase_gene_id, flybase_transcript_id, flybasename_gene, flybasename_transcript, goterm, hgnc_automatic_gene_name, hgnc_curated_gene_name, hgnc_symbol, id, id_noversion, infect, interproterm, last_modification_date, mgi_description, mgi_symbol, mirbase_accession, mirbase_gene_database, mirbase_gene_database_id, mirbase_id, mirbase_pubmedid, name, number_of_experiments, organism_part, otherconditions, phenotype, rgd, rgd_symbol, sgd_gene, sgd_transcript, symbol, synonym, tair_locus, tair_locus_model"
  return: "cell_line, cell_type, cint_jgi_v1, cint_jgi_v2, compound, creation_date, description, developmental_stage, disease, disease_state, domain_source, ensfamily_description, entrezgene, flybase_gene_id, flybase_transcript_id, flybasename_gene, flybasename_transcript, goterm, hgnc_automatic_gene_name, hgnc_curated_gene_name, hgnc_symbol, id, id_noversion, infect, interproterm, last_modification_date, mgi_description, mgi_symbol, mirbase_accession, mirbase_gene_database, mirbase_gene_database_id, mirbase_id, mirbase_pubmedid, name, number_of_experiments, organism_part, otherconditions, phenotype, rgd, rgd_symbol, sgd_gene, sgd_transcript, symbol, synonym, tair_locus, tair_locus_model"
  format: "text"
  hasaccession: "N"
]

DB biocatalogue [
  method: ebeye
  dbalias: biocatalogue


  [Part of this file has been deleted for brevity]

  fields: "acronym, anamorph, blast_name, common_name, domain_source, equivalent_name, genbank_acronym, genbank_anamorph, genbank_common_name, genbank_synonym, gene_code, id, in_part, includes, misnomer, misspelling, name, rank, synonym, teleomorph"
  return: "acronym, anamorph, blast_name, common_name, domain_source, equivalent_name, genbank_acronym, genbank_anamorph, genbank_common_name, genbank_synonym, gene_code, id, in_part, includes, misnomer, misspelling, name, rank, synonym, teleomorph"
  format: "text"
  hasaccession: "N"
]

DB uniparc [
  method: ebeye
  dbalias: uniparc
  fields: "domain_source, id, uniprotkb_exclusion"
  return: "domain_source, id, uniprotkb_exclusion"
  format: "text"
  hasaccession: "N"
]

DB uniprot [
  method: ebeye
  dbalias: uniprot
  fields: "acc, creation_date, dbRefProp_EMBL_protein_sequence_ID, dbRefProp_EcoGene_gene_designation, dbRefProp_EnsemblBacteria_protein_sequence_ID, dbRefProp_EnsemblFungi_protein_sequence_ID, dbRefProp_EnsemblMetazoa_protein_sequence_ID, dbRefProp_EnsemblPlants_protein_sequence_ID, dbRefProp_EnsemblProtists_protein_sequence_ID, dbRefProp_Ensembl_protein_sequence_ID, dbRefProp_FlyBase_gene_designation, dbRefProp_GeneFarm_family_ID, dbRefProp_GenomeReviews_gene_designation, dbRefProp_HGNC_gene_designation, dbRefProp_MGI_gene_designation, dbRefProp_RGD_gene_designation, dbRefProp_SGD_gene_designation, dbRefProp_WormBase_gene_designation, dbRefProp_WormBase_protein_sequence_ID, dbRefProp_ZFIN_gene_designation, dbRefProp_dictyBase_gene_designation, descAltName, descRecName, descSubName, description, domain_source, gene_ORF_name, gene_ordered_locus_name, gene_primary_name, gene_synonym_name, id, keywords, last_modification_date, organelle, organism_host_species, organism_lineage, organism_scientific_name, organism_species, protein_existence, references, sequence_fragment, sequence_last_modif_date, sequence_length, status"
  return: "acc, creation_date, dbRefProp_EMBL_protein_sequence_ID, dbRefProp_EcoGene_gene_designation, dbRefProp_EnsemblBacteria_protein_sequence_ID, dbRefProp_EnsemblFungi_protein_sequence_ID, dbRefProp_EnsemblMetazoa_protein_sequence_ID, dbRefProp_EnsemblPlants_protein_sequence_ID, dbRefProp_EnsemblProtists_protein_sequence_ID, dbRefProp_Ensembl_protein_sequence_ID, dbRefProp_FlyBase_gene_designation, dbRefProp_GeneFarm_family_ID, dbRefProp_GenomeReviews_gene_designation, dbRefProp_HGNC_gene_designation, dbRefProp_MGI_gene_designation, dbRefProp_RGD_gene_designation, dbRefProp_SGD_gene_designation, dbRefProp_WormBase_gene_designation, dbRefProp_WormBase_protein_sequence_ID, dbRefProp_ZFIN_gene_designation, dbRefProp_dictyBase_gene_designation, descAltName, descRecName, descSubName, description, domain_source, gene_ORF_name, gene_ordered_locus_name, gene_primary_name, gene_synonym_name, id, keywords, last_modification_date, organelle, organism_host_species, organism_lineage, organism_scientific_name, organism_species, protein_existence, references, sequence_fragment, sequence_last_modif_date, sequence_length, status"
  format: "text"
  hasaccession: "N"
]

DB uniref100 [
  method: ebeye
  dbalias: uniref100
  fields: "dbref_protein_name, dbref_source_organism, dbref_uniprotkb_id, domain_source, entry_common_taxon, id, last_modification_date, name"
  return: "domain_source, entry_common_taxon, id, last_modification_date, name"
  format: "text"
  hasaccession: "N"
]

DB uniref50 [
  method: ebeye
  dbalias: uniref50
  fields: "dbref_protein_name, dbref_source_organism, dbref_uniprotkb_id, domain_source, entry_common_taxon, id, last_modification_date, name"
  return: "domain_source, entry_common_taxon, id, last_modification_date, name"
  format: "text"
  hasaccession: "N"
]

DB uniref90 [
  method: ebeye
  dbalias: uniref90
  fields: "dbref_protein_name, dbref_source_organism, dbref_uniprotkb_id, domain_source, entry_common_taxon, id, last_modification_date, name"
  return: "domain_source, entry_common_taxon, id, last_modification_date, name"
  format: "text"
  hasaccession: "N"
]