EMBOSS: textget

| textget

## 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 text data entries

## Description

textget reads text data, usually from a named database, and writes a text file containing the original text of the entry or entries.

## Usage

Here is a sample session with textget

    % textget "srs:unilib:99"
    Get text data entries
    Text output file [outfile.text]:

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

## Command line arguments

    Get text data entries
    Version: EMBOSS:6.5.6.0

       Standard (Mandatory) qualifiers:
      [-text]              text       Text filename and optional format, or
                                      reference (input query)
      [-outfile]           outtext    (no help text) outtext value

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-text" associated qualifiers
       -iformat1           string     Input text 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     Text 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
[-text] (Parameter 1) | text | Text filename and optional format, or reference (input query) | Text entries |
[-outfile] (Parameter 2) | outtext | (no help text) outtext value | Text entries |
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-text" associated text qualifiers
-iformat1 -iformat_text | string | Input text format | Any string |
-iquery1 -iquery_text | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_text | integer | Input start position offset | Any integer value | 0
-idbname1 -idbname_text | string | User-provided database name | Any string |
"-outfile" associated outtext qualifiers
-odirectory2 -odirectory_outfile | string | Output directory | Any string |
-oformat2 -oformat_outfile | string | Text 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

## Input file format

The input is a standard EMBOSS text query.

The major text sources defined as standard in EMBOSS installations are non-standard types on the srs server and databases with a "text" query in the Data Resource Catalogue database DRCAT.

Data can also be read from text output in any supported text format written by an EMBOSS or third-party application. The text format is needed to identify the start and end of a single "entry" within a larger text file.

The input format can be specified by using the command-line qualifier `-format xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: text, html, xml (uniprotxml), obo, embl (swissprot)

See: http://emboss.sf.net/docs/themes/TextFormats.html for further information on text formats.

### Input files for usage example

### Database entry: "srs:unilib:99"

    > 99
    CGAP Lib id: 182
    Unigene id: 729
    dbEST lib id: 1452
    Keyword: lymph node
    Keyword: follicular lymphoma
    Keyword: non-normalized
    Keyword: bulk
    Keyword: CGAP
    Keyword: EST
    Keyword: Stratagene non-normalized
    Keyword: unknown developmental stage
    Keyword: size fractionated
    Keyword: directionally cloned
    Keyword: phagemid
    Keyword: oligo-dT primed
    Keyword: EST
    Keyword: CGAP
    Lib Name: NCI_CGAP_Lym5
    Organism: Homo sapiens
    Organ: lymph node
    Tissue_type: follicular lymphoma
    Lab host: SOLR (Stratagene, kanamycin resistant)
    Vector: pBluescript SK-
    Vector type: phagemid (ampicillin resistant)
    R. Site 1: EcoRI
    R. Site 2: XhoI
    Description: Cloned unidirectionally.  Primer: Oligo dT. Average insert size 1.2 kb. Non-amplified library. ~5' adaptor sequence: 5' GAATTCGGCACGAG 3' ~3' adaptor sequence: 5' CTCGAGTTTTTTTTTTTTTTTTTT 3'
    Library treatment: non-normalized
    Tissue description: Lymph node, follicular lymphoma, node 2
    Tissue supplier: Mark Raffeld, M.D.
    Sample type: Bulk
    Image legend:
    Producer: Stratagene, Inc.
    Clones generated to date: 2304
    Sequences generated to date: 1293

## Output file format

The output is a standard text 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: text, html, xml, json and list

See: http://emboss.sf.net/docs/themes/TextFormats.html for further information on text formats.

### Output files for usage example

### File: outfile.text

    > 99
    CGAP Lib id: 182
    Unigene id: 729
    dbEST lib id: 1452
    Keyword: lymph node
    Keyword: follicular lymphoma
    Keyword: non-normalized
    Keyword: bulk
    Keyword: CGAP
    Keyword: EST
    Keyword: Stratagene non-normalized
    Keyword: unknown developmental stage
    Keyword: size fractionated
    Keyword: directionally cloned
    Keyword: phagemid
    Keyword: oligo-dT primed
    Keyword: EST
    Keyword: CGAP
    Lib Name: NCI_CGAP_Lym5
    Organism: Homo sapiens
    Organ: lymph node
    Tissue_type: follicular lymphoma
    Lab host: SOLR (Stratagene, kanamycin resistant)
    Vector: pBluescript SK-
    Vector type: phagemid (ampicillin resistant)
    R. Site 1: EcoRI
    R. Site 2: XhoI
    Description: Cloned unidirectionally.  Primer: Oligo dT. Average insert size 1.2 kb. Non-amplified library. ~5' adaptor sequence: 5' GAATTCGGCACGAG 3' ~3' adaptor sequence: 5' CTCGAGTTTTTTTTTTTTTTTTTT 3'
    Library treatment: non-normalized
    Tissue description: Lymph node, follicular lymphoma, node 2
    Tissue supplier: Mark Raffeld, M.D.
    Sample type: Bulk
    Image legend:
    Producer: Stratagene, Inc.
    Clones generated to date: 2304
    Sequences generated to date: 1293

## Data files

None.

## 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
--- | ---
drtext | Get data resource entries complete text
entret | Retrieve sequence entries from flatfile databases and files
ontotext | Get ontology term(s) original full text
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