urlget



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Function

   Get URLs of data resources

Description

   Retrieves one or more URLs for further information about an identifier
   in a data resource.

   EMBOSS can retrieve specific data types (sequences, features, taxonomy,
   resources, ontology terms) as defined ACD types.

   Where there is no defined ACD inpu type, EMBOSS can retrieve the text
   of a database entry where the information is provided in a
   human-readable text format.

   For many data resources there is no retrievable data format. In these
   cases EMBOSS can use the Data Resource Catalogue to construct URLs that
   can be viewed in the user's preferred browser which should be able to
   render them in a meaningful way.

Algorithm

   urlget constructs the URL using the information in the Data Resource
   Catalogue entry which can be retrieved in its original format using
   drget.

   The Query records are searched to find a query that returns HTML data
   (not parseable as text). The user-supplied identifier is inserted in
   the query to construct a URL.

   If the identifier is specified as a swissprot (-swiss) or EMBL (-embl)
   cross-reference the defiitions of swissprot or EMBL cross-references in
   the DRCAT entry are used to select queries matching the identifier
   type.

   Alternatively, the EDAM term name describing the identifier can be
   provided by the user to resolve the selection from multiple queries.

Usage

   Here is a sample session with urlget


% urlget pseudocap:PA3363 -swiss
Get URLs of data resources
Url output file [pa3363.url]:


   Go to the output files for this example

Command line arguments

Get URLs of data resources
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-url]               url        Url filename and optional format, or
                                  reference (input query)
  [-outfile]           outurl     (no help text) outurl value

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-url" associated qualifiers
   -iformat1           string     Input URL format
   -idbname1           string     User-provided database name
   -swiss1             boolean    Swissprot cross-reference
   -embl1              boolean    EMBL/GenBank/DDBJ cross-reference
   -accession1         string     Primary accession for source data
   -identifier1        string     Identifier term name in EDAM

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     URL 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

   urlget reads a query containing a database name from DRCAT and an
   identifier.

Output file format

   urlget returns a file containing one or more URLs with a description.

   The -oformat qualifier provides a choice of formats which may be
   extended in future releases.

  Output files for usage example

  File: pa3363.url

http://www.pseudomonas.com/getAnnotation.do?locusID=PA3363        Locus ID (Pseu
doCAP): PA3363

Data files

   urlget uses the Data Resource Catalogue to retrieve information on URLs
   for the specified database name.

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

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