drtext

 

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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:6.4.0.0

   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
   -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  
-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 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.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 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.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 Retrieves 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