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 Generate 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: EMBL-Bank : No dbtype found supporting format emblxml-1.0 Warning: EMBL-Bank : No dbtype found supporting format emblxml-1.1 Warning: EMBLCDS : No dbtype found supporting format emblxml-1.1 Warning: EMBLCON : No dbtype found supporting format emblxml-1.0 Warning: EMBLCON : No dbtype found supporting format emblxml-1.1 Warning: EMBLCONEXP : No dbtype found supporting format emblxml-1.0 Warning: EMBLCONEXP : No dbtype found supporting format emblxml-1.1 Warning: Gene Ontology : No dbtype found supporting format oboxml Warning: Gene Ontology : No dbtype found supporting format gordfxml Warning: MEDLINE : No dbtype found supporting format pubmedxml Warning: Patent Equivalents : No dbtype found supporting format patent_equivalen ts Warning: No dbtype found for db Patent Equivalents Warning: Taxonomy : No dbtype found supporting format emboss_tax Warning: Taxonomy : No dbtype found supporting format ncbi_taxon Warning: UniParc : No dbtype found supporting format uniparcflat Go to the output files for this example Command line arguments Generate server cache file for Dbfetch/WSDbfetch data sources Version: EMBOSS:6.6.0.0 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 2013-07-15 12:00:00 DBNAME edam [ method: dbfetch hasacc: N format: "obo" edamfmt: "2549 ! OBO" edamdat: "2858 ! Ontology concept" edamtpc: "0091 ! Data handling" type: "text, obo" comment: "EMBRACE Data and Methods (EDAM) Ontology." example: "0338" example: "1929" example: "EDAM_operation:0338" example: "EDAM_format:1929" example: "0000338" example: "0001929" ] ALIAS edam_ontology edam ALIAS EDAM_data edam ALIAS EDAM_format edam ALIAS EDAM_identifier edam ALIAS EDAM_operation edam ALIAS EDAM_topic edam ALIAS MIR:00000189 edam DBNAME embl [ method: dbfetch hasacc: N format: "annot, embl, emblxml-1.2, entrysize, fasta, insdxml, seqxml" edamfmt: "1927 ! EMBL format" edamfmt: "2183 ! EMBLXML" edamfmt: "2330 ! Textual format" edamfmt: "1954 ! Pearson format" edamfmt: "2185 ! insdxml" edamfmt: "2332 ! XML" edamdat: "0855 ! Sequence metadata" edamdat: "2889 ! Sequence record full (nucleic acid)" edamdat: "1255 ! Feature record" edamdat: "2046 ! Sequence record lite (nucleic acid)" edamtpc: "3042 ! Nucleic acid sequences" type: "text, xml, sequence, features" 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." example: "M10051" example: "K00650" example: "D87894" example: "AJ242600" example: "J00231.1" example: "K00650.1" [Part of this file has been deleted for brevity] DBNAME unisave [ method: dbfetch hasacc: N format: "annot, entrysize, fasta, uniprot" edamfmt: "1963 ! UniProtKB format" edamfmt: "2330 ! Textual format" edamfmt: "1954 ! Pearson format" edamdat: "0855 ! Sequence metadata" edamdat: "1255 ! Feature record" edamdat: "2047 ! Sequence record lite (protein)" edamdat: "2888 ! Sequence record full (protein)" edamtpc: "3043 ! Protein sequences" type: "text, features, sequence" comment: "The UniProtKB Sequence/Annotation Version Archive (UniSave) is a rep ository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions." example: "P06213" example: "P06213.157" example: "P06213.3" example: "INSR_HUMAN" ] ALIAS uniprotkb_sequence_annotation_version_archive unisave ALIAS DRCAT:UniSave unisave DBNAME uspto_prt [ method: dbfetch hasacc: N format: "annot, embl, entrysize, fasta, seqxml" edamfmt: "1927 ! EMBL format" edamfmt: "2330 ! Textual format" edamfmt: "1954 ! Pearson format" edamfmt: "2332 ! XML" edamdat: "0855 ! Sequence metadata" edamdat: "2888 ! Sequence record full (protein)" edamdat: "1255 ! Feature record" edamdat: "2047 ! Sequence record lite (protein)" edamtpc: "3043 ! Protein sequences" type: "text, xml, sequence, features" comment: "Protein sequences appearing in patents from the United States Patent and Trademark Office (USPTO)." example: "AAA00053" example: "I02590" example: "AAA00053.1" ] ALIAS uspto_patent_proteins uspto_prt ALIAS uspto_proteins uspto_prt ALIAS usptoprt uspto_prt ALIAS uspop uspto_prt ALIAS uspo_prt uspto_prt ALIAS uspto uspto_prt 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 cacheebeyesearch Generate server cache file for EB-eye search domains 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 (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