EMBOSS: urlget

| urlget

## Wiki

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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:6.5.6.0

       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