                                   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:6.5.6.0

   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


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)

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
