EMBOSS: drtext

| drtext

## 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 complete text

## Description

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.

## Usage

Here is a sample session with drtext

    % drtext drcat:uniprot
    Get data resource entries complete text
    Full text output file [uniprot.drtext]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

    Get data resource entries complete text
    Version: EMBOSS:6.5.6.0

       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

## Input file format

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.

### 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

drtext reports the full text of the input resources.

### Output files for usage example

### File: uniprot.drtext

    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
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)

## 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