cachedbfetch 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 Dbfetch/WSDbfetch data sources Description Contacts the EBI dbfetch service to find the available databases and saves definitions for them to a server cache file. Usage Here is a sample session with cachedbfetch % cachedbfetch -servername tdbfetch -auto -cachefile ~/.embossdata/qatests.serve r.tdbfetch Warning: No dbtype found supporting format emblxml-1.2 Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format emblxml Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format insdxml Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format emblxml-1.2 Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format emblxml Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format emblxml-1.2 Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format emblxml Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format insdxml Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format emblxml-1.2 Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format csv Warning: No dbtype found supporting format tab Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format tab Warning: No dbtype found for db HGNC Warning: No dbtype found supporting format hgbase Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format interpro Warning: No dbtype found supporting format interproxml Warning: No dbtype found for db InterPro Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format iprmc Warning: No dbtype found supporting format iprmctab Warning: No dbtype found supporting format iprmcxml Warning: No dbtype found for db IPRMC Warning: No dbtype found supporting format iprmc Warning: No dbtype found supporting format iprmctab Warning: No dbtype found supporting format iprmcxml Warning: No dbtype found for db IPRMC UniParc Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format livelists Warning: No dbtype found for db LiveLists Warning: No dbtype found supporting format bibtex Warning: No dbtype found supporting format endnote Warning: No dbtype found supporting format isi Warning: No dbtype found supporting format medlinefull Warning: No dbtype found supporting format medlineref Warning: No dbtype found supporting format medlinexml Warning: No dbtype found supporting format modsxml Warning: No dbtype found supporting format ris Warning: No dbtype found supporting format wordbibxml Warning: No dbtype found for db MEDLINE Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format nrl1 Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format nrl2 Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format nrl1 Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format nrl2 Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format mmcif Warning: No dbtype found supporting format pdbml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format resid Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format sgtxml Warning: No dbtype found supporting format taxonomy Warning: No dbtype found supporting format enataxonomyxml Warning: No dbtype found supporting format uniprottaxonomyrdfxml Warning: No dbtype found for db Taxonomy Warning: No dbtype found supporting format tracexml Warning: No dbtype found supporting format uniparc Warning: No dbtype found supporting format uniprotrdfxml Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format uniprotrdfxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format uniprotrdfxml Warning: No dbtype found supporting format uniref100 Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format uniprotrdfxml Warning: No dbtype found supporting format uniref50 Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format uniprotrdfxml Warning: No dbtype found supporting format uniref90 Warning: No dbtype found supporting format seqxml Warning: No dbtype found supporting format annot Warning: No dbtype found supporting format entrysize Warning: No dbtype found supporting format seqxml Go to the output files for this example Command line arguments Generates server cache file for Dbfetch/WSDbfetch data sources Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-servername] string [dbfetch] Name of the ws/dbfetch server defined in EMBOSS resource files (Any string) [-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 -odirectory2 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 cachedbfetch contacts the EBI dbfetch server for details of available databases. Output file format cachedbfetch 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.tdbfetch # qatests.server.tdbfetch 2011-07-15 12:00:00 DB edam [ method: dbfetch hasacc: N format: "obo" type: "text, obo" example: "0000352, 0001223" comment: "EMBRACE Data and Methods (EDAM) Ontology." ] DB embl [ method: dbfetch hasacc: N format: "embl, fasta" type: "text, sequence, features" example: "M10051, K00650, D87894, AJ242600, HSINSR, HSFOS, ROD894, LOP242600, J00231.1, K00650.1, D87894.1, AJ242600.1" comment: "EMBL Nucleotide Sequence Database, Europe's primary nucleotide seque nce resource. The main sources of the DNA and RNA sequences in the database are submissions from individual researchers, genome sequencing projects and patent a pplications." ] DB emblcds [ method: dbfetch hasacc: N format: "embl, fasta" type: "text, sequence, features" example: "AAA59452, AAA59452.1" comment: "EMBLCDS is a database of nucleotide sequences of the CDS (coding seq uence) features, as annotated in EMBL database. EMBLCDS record contains the nucl eotide sequence of the CDS region, accompanying annotation from the parent nucle otide entry and the additional automatically generated annotation." ] DB emblcon [ method: dbfetch hasacc: N format: "embl, fasta" type: "text, sequence, features" example: "CH003588, CH003588.1" comment: "The EMBLCON database division represents complete genomes and other long sequences constructed from segment entries." ] DB emblconexp [ method: dbfetch hasacc: N format: "embl, fasta" type: "text, sequence, features" example: "AL672111, AL672111.1" comment: "The EMBLCON database division represents complete genomes and other long sequences constructed from segment entries. Expanded entries including the complete sequence." ] DB emblsva [ method: dbfetch hasacc: N [Part of this file has been deleted for brevity] format: "fasta, gff3, uniprot, uniprotxml" type: "text, features, sequence" example: "P06213, P29306, P68255, INSR_HUMAN, 1433X_MAIZE, 1433T_RAT" comment: "The UniProt Knowledgebase (UniProtKB) is the central access point fo r extensive curated protein information, including function, classification, and cross-references. Search UniProtKB to retrieve aEURoeeverything that is knownaE UR about a particular sequence." ] DB uniref100 [ method: dbfetch hasacc: N format: "fasta" type: "sequence" example: "UniRef100_P06213" comment: "The UniProt Reference Clusters (UniRef) databases combine closely re lated sequences into a single record to speed searches. There are three differen t non-redundant databases with different sequence identity cut-offs. In UniRef10 0, UniRef90 and UniRef50 databases no pair of sequences in the representative se t has >100%, >90% or >50% mutual sequence identity. The three UniRef databases a llow the user to choose between a fast search and a truly comprehensive one." ] DB uniref50 [ method: dbfetch hasacc: N format: "fasta" type: "sequence" example: "UniRef50_P06213" comment: "The UniProt Reference Clusters (UniRef) databases combine closely re lated sequences into a single record to speed searches. There are three differen t non-redundant databases with different sequence identity cut-offs. In UniRef10 0, UniRef90 and UniRef50 databases no pair of sequences in the representative se t has >100%, >90% or >50% mutual sequence identity. The three UniRef databases a llow the user to choose between a fast search and a truly comprehensive one." ] DB uniref90 [ method: dbfetch hasacc: N format: "fasta" type: "sequence" example: "UniRef90_P06213" comment: "The UniProt Reference Clusters (UniRef) databases combine closely re lated sequences into a single record to speed searches. There are three differen t non-redundant databases with different sequence identity cut-offs. In UniRef10 0, UniRef90 and UniRef50 databases no pair of sequences in the representative se t has >100%, >90% or >50% mutual sequence identity. The three UniRef databases a llow the user to choose between a fast search and a truly comprehensive one." ] DB unisave [ method: dbfetch hasacc: N format: "fasta, uniprot" type: "text, features, sequence" example: "P06213, P06213.157, P06213.3, INSR_HUMAN" comment: "The UniProtKB Sequence/Annotation Version Archive (UniSave) is a rep ository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions." ] DB uspto_prt [ method: dbfetch hasacc: N format: "embl, fasta" type: "text, sequence, features" example: "AAA00053, I02590, AAA00053.1" comment: "Protein sequences appearing in patents from the United States Patent and Trademark Office (USPTO)." ] 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 cacheebeyesearch Generates server cache file for EB-eye search domains 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