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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:6.6.0.0
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
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' adapt
or 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' adapt
or 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)
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
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