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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
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