cacheebeyesearch |
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% cacheebeyesearch -cachefile ~/.embossdata/qatests.server.ebeye -auto |
Go to the output files for this example
Generates server cache file for EB-eye search domains Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-cachefile] outfile [server.$(servername)] Server cache output file Additional (Optional) qualifiers: -outfile outfile [stdout] Output file name Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outfile" associated qualifiers -odirectory string Output directory "-cachefile" associated qualifiers -odirectory1 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-cachefile] (Parameter 1) |
outfile | Server cache output file | Output file | server.$(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 |
# 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" ] |
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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.