drtext |
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drtext reads one or more complete data resource entries from a database or a file and writes them to a text file. Optionally, the first data resourcefrom the input stream only can be retrieved. The complete entry, including heading annotation, is retrieved and written and the data is not altered or reformatted in any way.
% drtext drcat:uniprot Get data resource entries complete text Full text output file [uniprot.drtext]: |
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Get data resource entries complete text Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-resources] resource Data resource filename and optional format, or reference (input query) [-outfile] outfile [*.drtext] Full text output file 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 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) |
outfile | Full text output file | Output file | <*>.drtext |
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 outfile qualifiers | ||||
-odirectory2 -odirectory_outfile |
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 |
The input is a standard EMBOSS resource query.
The expected source of data resource information is the Data Resource Catalogue database "drcat" which is available as a standard database in all EMBOSS installations.
Data can also be read from resource output in "drcat" format written by an EMBOSS application.
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 |
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 |
drget | Get data resource entries |
entret | Retrieve sequence entries from flatfile databases and files |
ontotext | Get ontology term(s) original full text |
textget | Get text data entries |
textsearch | Search the textual description of sequence(s) |
xmltext | Get XML document original full text |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.