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 resturns 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:6.4.0.0

   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
   -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 0000639 | Protein sequences
EDAMdat 0002201 | Sequence record full
EDAMid  0003021 | UniProt accession
EDAMfmt 0001929 | FASTA format
EDAMfmt 0002376 | RDF
EDAMfmt 0002188 | uniprot
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | 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 0000639 | Protein sequences
EDAMdat 0002201 | Sequence record full
EDAMid  0003021 | UniProt accession
EDAMfmt 0001929 | FASTA format
EDAMfmt 0002376 | RDF
EDAMfmt 0002188 | uniprot
EDAMfmt 0002331 | HTML
EDAMfmt 0002332 | 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