urlget

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Function

Description

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

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

% 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

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

Output file format

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

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

Comments