cacheebeyesearch Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Generates 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 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 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 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_modifica tion_date, name, nonsense-mediated_decay, polya_site, protein, transcription_sta rt_site, tss_cluster" return: "description, exon, id, intron, keywords, last_modification_date, name , nonsense-mediated_decay, polya_site, protein, transcription_start_site, tss_cl uster" 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_da te, description, developmental_stage, disease, disease_state, domain_source, ens family_description, entrezgene, flybase_gene_id, flybase_transcript_id, flybasen ame_gene, flybasename_transcript, goterm, hgnc_automatic_gene_name, hgnc_curated _gene_name, hgnc_symbol, id, id_noversion, infect, interproterm, last_modificati on_date, mgi_description, mgi_symbol, mirbase_accession, mirbase_gene_database, mirbase_gene_database_id, mirbase_id, mirbase_pubmedid, name, number_of_experime nts, organism_part, otherconditions, phenotype, rgd, rgd_symbol, sgd_gene, sgd_t ranscript, symbol, synonym, tair_locus, tair_locus_model" return: "cell_line, cell_type, cint_jgi_v1, cint_jgi_v2, compound, creation_da te, description, developmental_stage, disease, disease_state, domain_source, ens family_description, entrezgene, flybase_gene_id, flybase_transcript_id, flybasen ame_gene, flybasename_transcript, goterm, hgnc_automatic_gene_name, hgnc_curated _gene_name, hgnc_symbol, id, id_noversion, infect, interproterm, last_modificati on_date, mgi_description, mgi_symbol, mirbase_accession, mirbase_gene_database, mirbase_gene_database_id, mirbase_id, mirbase_pubmedid, name, number_of_experime nts, organism_part, otherconditions, phenotype, rgd, rgd_symbol, sgd_gene, sgd_t ranscript, 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, te leomorph" 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, te leomorph" 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_Eco Gene_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_s equence_ID, dbRefProp_Ensembl_protein_sequence_ID, dbRefProp_FlyBase_gene_design ation, dbRefProp_GeneFarm_family_ID, dbRefProp_GenomeReviews_gene_designation, d bRefProp_HGNC_gene_designation, dbRefProp_MGI_gene_designation, dbRefProp_RGD_ge ne_designation, dbRefProp_SGD_gene_designation, dbRefProp_WormBase_gene_designat ion, dbRefProp_WormBase_protein_sequence_ID, dbRefProp_ZFIN_gene_designation, db RefProp_dictyBase_gene_designation, descAltName, descRecName, descSubName, descr iption, domain_source, gene_ORF_name, gene_ordered_locus_name, gene_primary_name , gene_synonym_name, id, keywords, last_modification_date, organelle, organism_h ost_species, organism_lineage, organism_scientific_name, organism_species, prote in_existence, references, sequence_fragment, sequence_last_modif_date, sequence_ length, status" return: "acc, creation_date, dbRefProp_EMBL_protein_sequence_ID, dbRefProp_Eco Gene_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_s equence_ID, dbRefProp_Ensembl_protein_sequence_ID, dbRefProp_FlyBase_gene_design ation, dbRefProp_GeneFarm_family_ID, dbRefProp_GenomeReviews_gene_designation, d bRefProp_HGNC_gene_designation, dbRefProp_MGI_gene_designation, dbRefProp_RGD_ge ne_designation, dbRefProp_SGD_gene_designation, dbRefProp_WormBase_gene_designat ion, dbRefProp_WormBase_protein_sequence_ID, dbRefProp_ZFIN_gene_designation, db RefProp_dictyBase_gene_designation, descAltName, descRecName, descSubName, descr iption, domain_source, gene_ORF_name, gene_ordered_locus_name, gene_primary_name , gene_synonym_name, id, keywords, last_modification_date, organelle, organism_h ost_species, organism_lineage, organism_scientific_name, organism_species, prote in_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" ] 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 Generates server cache file for DAS servers or for the DAS registry cachedbfetch Generates server cache file for Dbfetch/WSDbfetch data sources cacheensembl Generates server cache file for an Ensembl server dbtell Display information about a public database servertell Display information about a public server showdb Displays information on configured databases showserver Displays 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