                                   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:6.6.0.0

   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


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.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

   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.uni
prot.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)
                    xmltext        Get XML document original full 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
