textget

 

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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

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)
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 © 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