|
|
drget |
Please help by correcting and extending the Wiki pages.
% 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
Get data resource entries
Version: EMBOSS:6.5.6.0
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 |
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 |
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.
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 |
| 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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.