                                cachedbfetch



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   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
