                                cachedbfetch



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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: 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 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 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 tab
Warning: No dbtype found for db IPI History
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 insdxml
Warning: No dbtype found supporting format tinyseq
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 insdxml
Warning: No dbtype found supporting format tinyseq
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

Generate server cache file for Dbfetch/WSDbfetch data sources
Version: EMBOSS:6.5.6.0

   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 2012-07-15 12:00:00

DB edam [
  method: dbfetch
  hasacc: N
  format: "obo"
  edamfmt: "EDAM_format:2549"
  edamdat: "EDAM_data:2858"
  edamtpc: "EDAM_topic:0770"
  type: "text, obo"
  example: "0338, 1929, EDAM_operation:0338, EDAM_format:1929, 0000338, 0001929"
  comment: "EMBRACE Data and Methods (EDAM) Ontology."
]

DB embl [
  method: dbfetch
  hasacc: N
  format: "embl, fasta"
  edamfmt: "EDAM_format:1927, EDAM_format:2183, EDAM_format:1954, EDAM_format:23
30, EDAM_format:2185, EDAM_format:2332"
  edamdat: "EDAM_data:2889, EDAM_data:2046, EDAM_data:0855, EDAM_data:2018"
  edamtpc: "EDAM_topic:3042"
  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"
  edamfmt: "EDAM_format:1927, EDAM_format:2184, EDAM_format:1954, EDAM_format:23
30, EDAM_format:2332"
  edamdat: "EDAM_data:2889, EDAM_data:2046, EDAM_data:0855, EDAM_data:2018"
  edamtpc: "EDAM_topic:3042"
  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"
  edamfmt: "EDAM_format:1927, EDAM_format:2183, EDAM_format:1954, EDAM_format:23
30, EDAM_format:2185, EDAM_format:2332"
  edamdat: "EDAM_data:2889, EDAM_data:2046, EDAM_data:0855, EDAM_data:2018"
  edamtpc: "EDAM_topic:3042"
  type: "text, sequence, features"
  example: "CH003588, CH003588.1"
  comment: "The EMBLCON database division represents complete genomes and other
long sequences constructed from segment entries."
]



  [Part of this file has been deleted for brevity]

  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"
  edamfmt: "EDAM_format:1954, EDAM_format:2332"
  edamdat: "EDAM_data:2047, EDAM_data:0849, EDAM_data:2888"
  edamtpc: "EDAM_topic:3043"
  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"
  edamfmt: "EDAM_format:1954, EDAM_format:2332"
  edamdat: "EDAM_data:2047, EDAM_data:0849, EDAM_data:2888"
  edamtpc: "EDAM_topic:3043"
  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"
  edamfmt: "EDAM_format:1954, EDAM_format:1977"
  edamdat: "EDAM_data:2047, EDAM_data:2888"
  edamtpc: "EDAM_topic:3043"
  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"
  edamfmt: "EDAM_format:1927, EDAM_format:2330, EDAM_format:1954, EDAM_format:23
32"
  edamdat: "EDAM_data:0855, EDAM_data:2888, EDAM_data:2018, EDAM_data:2047"
  edamtpc: "EDAM_topic:3043"
  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         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
