urlget

 

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 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:6.5.0.0

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-url]
(Parameter 1)
url Url filename and optional format, or reference (input query) URL entries  
[-outfile]
(Parameter 2)
outurl (no help text) outurl value URL entries  
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-url" associated url qualifiers
-iformat1
-iformat_url
string Input URL format Any string  
-idbname1
-idbname_url
string User-provided database name Any string  
-swiss1
-swiss_url
boolean Swissprot cross-reference Boolean value Yes/No N
-embl1
-embl_url
boolean EMBL/GenBank/DDBJ cross-reference Boolean value Yes/No N
-accession1
-accession_url
string Primary accession for source data Any string  
-identifier1
-identifier_url
string Identifier term name in EDAM Any string  
"-outfile" associated outurl qualifiers
-odirectory2
-odirectory_outfile
string Output directory Any string  
-oformat2
-oformat_outfile
string URL 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

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 (PseudoCAP): 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 © 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