|   | textget | 
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| % textget "srs:unilib:99" Get text data entries Text output file [outfile.text]: | 
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Go to the output files for this example
| 
Get text data entries
Version: EMBOSS:6.6.0.0
   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 | 
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.
| > 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 | 
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.
| > 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 | 
| 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) | 
| 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.