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:6.5.0.0

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-cachefile]
(Parameter 1)
outfile Server cache output file Output file server.$(servername)
Additional (Optional) qualifiers
-outfile outfile Output file name Output file stdout
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory string Output directory Any string  
"-cachefile" associated outfile qualifiers
-odirectory1
-odirectory_cachefile
string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 2012-07-15 12:00:00

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

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

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

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

DB chebi [
  method: ebeye
  dbalias: chebi


  [Part of this file has been deleted for brevity]

  fields: "EMBLWGS_version, EMBL_CON_version, EMBL_TPA_version, EMBL_version, EPO_version, H_INV_version, IPI_version, REFSEQ_version, USPTO_version, UniProtKB/Swiss-Prot_version, UniProtKB/TrEMBL_version, domain_source, id, uniprotkb_exclusion"
  return: "domain_source, id"
  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_PATRIC_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, descAltName, descRecName, descSubName, domain_source, gene_primary_name, id, organism_scientific_name, 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, id, 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, id, 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, id, name"
  format: "text"
  hasaccession: "N"
]

DB wgs_masters [
  method: ebeye
  dbalias: wgs_masters
  fields: "description, domain_source, id, name, scientific_name"
  return: "description, domain_source, id, name, scientific_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 © 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