cacheebeyesearch



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Function

   Generate server cache file for EB-eye search domains

Description

   Contacts the EBI wsebeyesearch service to find the available databases
   and saves definitions for them to a server cache file.

Usage

   Here is a sample session with cacheebeyesearch


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


   Go to the output files for this example

Command line arguments

Generate server cache file for EB-eye search domains
Version: EMBOSS:6.6.0.0

   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


Input file format

   cacheebeyesearchcontacts the EBI wsebeyesearch service for details of
   available databases.

Output file format

   cacheebeyesearch writes a server cache file which can be saved in the
   user's .embossdata directory or, for a system administrator, stored in
   the site-wide share/EMBOSS/ directory.

  Output files for usage example

  File: qatests.server.ebeye

# qatests.server.ebeye 2013-07-15 12:00:00

DBNAME arrayexpress_repository [
  method: "ebeye"
  dbalias: "arrayexpress-repository"
  fields: "$facets, acc, author, biomaterial-characteristics, description, domai
n_source, experimentalfactors-factorvalues, id, keywords, last_update_date, name
, release_date, submission_date"
  return: "acc, description, domain_source, id, name"
  format: "text"
  hasaccession: "N"
]

DBNAME atlas_experiments [
  method: "ebeye"
  dbalias: "atlas-experiments"
  fields: "$facets, creation_date, description, domain_source, id, last_modifica
tion_date, name"
  return: "description, domain_source, id, name"
  format: "text"
  hasaccession: "N"
]

DBNAME atlas_genes [
  method: "ebeye"
  dbalias: "atlas-genes"
  fields: "$facets, cell_line, cell_type, compound, creation_date, description,
developmental_stage, disease, disease_state, domain_source, ensfamily_descriptio
n, entrezgene, flybase_gene_id, flybase_transcript_id, flybasename_gene, flybase
name_transcript, gene_biotype, goterm, hgnc_symbol, id, id_noversion, infect, in
terproterm, last_modification_date, mgi_description, mgi_symbol, mirbase_accessi
on, mirbase_accession_number, mirbase_description, mirbase_gene_database, mirbas
e_gene_database_id, mirbase_id, mirbase_matured_mirna, mirbase_pubmedid, mirbase
_sequence, name, number_of_experiments, organism_part, otherconditions, pathwayi
d, pathwayname, phenotype, rgd, rgd_symbol, synonym"
  return: "cell_line, cell_type, compound, description, developmental_stage, dis
ease_state, domain_source, id, infect, name, number_of_experiments, organism_par
t, otherconditions, phenotype"
  format: "text"
  hasaccession: "N"
]

DBNAME biocatalogue [
  method: "ebeye"
  dbalias: "biocatalogue"
  fields: "$facets, acc, creation_date, description, domain_source, id, keywords
, last_modification_date, name, provider, service_types"
  return: "description, domain_source, id, keywords, name, provider, service_typ
es"
  format: "text"
  hasaccession: "N"
]

DBNAME biomodels [
  method: "ebeye"
  dbalias: "biomodels"
  fields: "$facets, acc, author, creation_date, curated, description, domain_sou
rce, id, keywords, last_modification_date, name, original_model"
  return: "description, domain_source, id, name"
  format: "text"
  hasaccession: "N"
]

DBNAME chebi [
  method: "ebeye"
  dbalias: "chebi"


  [Part of this file has been deleted for brevity]

  fields: "$facets, acc, creation_date, dbRefProp_EMBL_protein_sequence_ID, dbRe
fProp_EcoGene_gene_designation, dbRefProp_EnsemblBacteria_protein_sequence_ID, d
bRefProp_EnsemblFungi_protein_sequence_ID, dbRefProp_EnsemblMetazoa_protein_sequ
ence_ID, dbRefProp_EnsemblPlants_protein_sequence_ID, dbRefProp_EnsemblProtists_
protein_sequence_ID, dbRefProp_Ensembl_protein_sequence_ID, dbRefProp_FlyBase_ge
ne_designation, dbRefProp_GeneFarm_family_ID, dbRefProp_HGNC_gene_designation, d
bRefProp_MGI_gene_designation, dbRefProp_PATRIC_gene_designation, dbRefProp_RGD_
gene_designation, dbRefProp_SGD_gene_designation, dbRefProp_WormBase_gene_design
ation, dbRefProp_WormBase_protein_sequence_ID, dbRefProp_ZFIN_gene_designation,
dbRefProp_dictyBase_gene_designation, descAltName, descRecName, descSubName, des
cription, domain_source, gene_ORF_name, gene_ordered_locus_name, gene_primary_na
me, gene_synonym_name, id, keyword_id, keywords, last_modification_date, organel
le, organism_host_species, organism_lineage, organism_scientific_name, organism_
species, protein_existence, references, sequence_fragment, sequence_last_modif_d
ate, sequence_length, status"
  return: "acc, descAltName, descRecName, descSubName, domain_source, gene_prima
ry_name, id, organism_scientific_name, sequence_length, status"
  format: "text"
  hasaccession: "N"
]

DBNAME uniref100 [
  method: "ebeye"
  dbalias: "uniref100"
  fields: "$facets, dbref_protein_name, dbref_source_organism, dbref_uniprotkb_i
d, domain_source, entry_common_taxon, id, last_modification_date, name"
  return: "domain_source, id, name"
  format: "text"
  hasaccession: "N"
]

DBNAME uniref50 [
  method: "ebeye"
  dbalias: "uniref50"
  fields: "$facets, dbref_protein_name, dbref_source_organism, dbref_uniprotkb_i
d, domain_source, entry_common_taxon, id, last_modification_date, name"
  return: "domain_source, id, name"
  format: "text"
  hasaccession: "N"
]

DBNAME uniref90 [
  method: "ebeye"
  dbalias: "uniref90"
  fields: "$facets, dbref_protein_name, dbref_source_organism, dbref_uniprotkb_i
d, domain_source, entry_common_taxon, id, last_modification_date, name"
  return: "domain_source, id, name"
  format: "text"
  hasaccession: "N"
]

DBNAME uspto [
  method: "ebeye"
  dbalias: "uspto"
  fields: "$facets, acc, creation_date, data_class, description, doc_file, domai
n_source, id, length, offset_end, offset_start, organism, organism_species, refe
rences, sequence_version"
  return: "acc, description, doc_file, domain_source, id, offset_end, offset_sta
rt"
  format: "text"
  hasaccession: "N"
]

DBNAME wgs_masters [
  method: "ebeye"
  dbalias: "wgs_masters"
  fields: "$facets, description, domain_source, id, name"
  return: "description, domain_source, id, name"
  format: "text"
  hasaccession: "N"
]


Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   cachedas         Generate server cache file for DAS servers or for the DAS
                    registry
   cachedbfetch     Generate server cache file for Dbfetch/WSDbfetch data
                    sources
   cacheensembl     Generate server cache file for an Ensembl server
   dbtell           Display information about a public database
   servertell       Display information about a public server
   showdb           Display information on configured databases
   showserver       Display information on configured servers

Author(s)

   Peter Rice
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None