EMBOSS: cachedbfetch

| 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.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 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

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 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:2330, 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 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"
      edamfmt: "EDAM_format:1927, EDAM_format:2184, EDAM_format:1954, EDAM_format:2330, 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 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"
      edamfmt: "EDAM_format:1927, EDAM_format:2183, EDAM_format:1954, EDAM_format:2330, 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 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"
      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 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"
      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 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"
      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 repository 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:2332"
      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 © 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