EMBOSS: cacheebeyesearch

| cacheebeyesearch

## Wiki

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Please help by correcting and extending the Wiki pages.

## 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:6.5.6.0

       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