drget

 

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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:6.5.0.0

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-resources]
(Parameter 1)
resource Data resource filename and optional format, or reference (input query) Data resource catalogue entry(s)  
[-outfile]
(Parameter 2)
outresource Output data resource file name Data resource entry <*>.drget
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-resources" associated resource qualifiers
-iformat1
-iformat_resources
string Input resource format Any string  
-iquery1
-iquery_resources
string Input query fields or ID list Any string  
-ioffset1
-ioffset_resources
integer Input start position offset Any integer value 0
-idbname1
-idbname_resources
string User-provided database name Any string  
"-outfile" associated outresource qualifiers
-odirectory2
-odirectory_outfile
string Output directory Any string  
-oformat2
-oformat_outfile
string Data resource output format 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

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.org/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.uniprot.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.org/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.uniprot.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 © 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