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drget
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
Get data resource entries
Description
Searches a database of data resources and returns matching entries.
Usage
Here is a sample session with drget
% drget drcat:uniprot
Get data resource entries
Data resource output file [uniprot.drcat]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
Get data resource entries
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-resources] resource Data resource filename and optional format,
or reference (input query)
[-outfile] outresource [*.drget] Output data resource file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-resources" associated qualifiers
-iformat1 string Input resource format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-idbname1 string User-provided database name
"-outfile" associated qualifiers
-odirectory2 string Output directory
-oformat2 string Data resource output format
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
drget reads any data resource query.
Input files for usage example
Database entry: drcat:uniprot
ID UniProt
IDalt UniProtKB
Name Universal protein resource
Desc A comprehensive, high-quality and freely accessible resource of protein
sequence and functional information.
URL http://www.uniprot.org/
Taxon 1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid 3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2188 | uniprot
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref SP_FT | None
Query Sequence record full | HTML | UniProt accession | http://www.uniprot.or
g/uniprot/%s
Query Sequence record full | uniprot | UniProt accession | http://www.uniprot
.org/uniprot/%s.txt
Query Sequence record full | XML | UniProt accession | http://www.uniprot.org
/uniprot/%s.xml
Query Sequence record full | RDF | UniProt accession | http://www.uniprot.org
/uniprot/%s.rdf
Query Sequence record full | FASTA format | UniProt accession | http://www.un
iprot.org/uniprot/%s.fasta
Example UniProt accession | P12345
Output file format
The output is a standard EMBOSS resource file.
The results can be output in one of several styles by using the
command-line qualifier -oformat xxx, where 'xxx' is replaced by the
name of the required format. The available format names are: drcat,
basic, wsbasic, list.
See: http://emboss.sf.net/docs/themes/ResourceFormats.html for further
information on resource formats.
Output files for usage example
File: uniprot.drcat
ID UniProt
IDalt UniProtKB
Name Universal protein resource
Desc A comprehensive, high-quality and freely accessible resource of protein
sequence and functional information.
URL http://www.uniprot.org/
Taxon 1 | all
EDAMtpc 0639 | Protein sequence analysis
EDAMdat 2201 | Sequence record full
EDAMid 3021 | UniProt accession
EDAMfmt 1929 | FASTA format
EDAMfmt 2376 | RDF
EDAMfmt 2188 | uniprot
EDAMfmt 2331 | HTML
EDAMfmt 2332 | XML
Xref SP_FT | None
Query Sequence record full | HTML | UniProt accession | http://www.uniprot.or
g/uniprot/%s
Query Sequence record full | uniprot | UniProt accession | http://www.uniprot
.org/uniprot/%s.txt
Query Sequence record full | XML | UniProt accession | http://www.uniprot.org
/uniprot/%s.xml
Query Sequence record full | RDF | UniProt accession | http://www.uniprot.org
/uniprot/%s.rdf
Query Sequence record full | FASTA format | UniProt accession | http://www.un
iprot.org/uniprot/%s.fasta
Example UniProt accession | P12345
Data files
The Data Resource Catalogue is included in EMBOSS as local database
drcat.
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
drfinddata Find public databases by data type
drfindformat Find public databases by format
drfindid Find public databases by identifier
drfindresource Find public databases by resource
drtext Get data resource entries complete text
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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