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textget |
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% 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
Get text data entries
Version: EMBOSS:6.4.0.0
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
-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
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| 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 | |
| -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 | Retrieves sequence entries from flatfile databases and files |
| ontotext | Get ontology term(s) original full text |
| textsearch | Search the textual description of sequence(s) |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.