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.server.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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-servername]
(Parameter 1)		 string Name of the ws/dbfetch server defined in EMBOSS resource files Any string dbfetch
[-cachefile]
(Parameter 2)		 outfile Server cache output file Output file server.$(servername)
Additional (Optional) qualifiers
-outfile outfile Output file name Output file stdout
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory string Output directory Any string  
"-cachefile" associated outfile qualifiers
-odirectory2
-odirectory_cachefile		 string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 sequence resource. The main sources of the DNA and RNA sequences in the database are submissions from individual researchers, genome sequencing projects and patent applications."
]

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 sequence) features, as annotated in EMBL database. EMBLCDS record contains the nucleotide sequence of the CDS region, accompanying annotation from the parent nucleotide 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 for extensive curated protein information, including function, classification, and cross-references. Search UniProtKB to retrieve “everything that is known” 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 related sequences into a single record to speed searches. There are three different non-redundant databases with different sequence identity cut-offs. In UniRef100, UniRef90 and UniRef50 databases no pair of sequences in the representative set has >100%, >90% or >50% mutual sequence identity. The three UniRef databases allow 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 related sequences into a single record to speed searches. There are three different non-redundant databases with different sequence identity cut-offs. In UniRef100, UniRef90 and UniRef50 databases no pair of sequences in the representative set has >100%, >90% or >50% mutual sequence identity. The three UniRef databases allow 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 related sequences into a single record to speed searches. There are three different non-redundant databases with different sequence identity cut-offs. In UniRef100, UniRef90 and UniRef50 databases no pair of sequences in the representative set has >100%, >90% or >50% mutual sequence identity. The three UniRef databases allow 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 repository 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 © 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