view release on metacpan or  search on metacpan

GMOD/StandardURLs.pm  view on Meta::CPAN

=item $mod->fetch(@options);

Fetch the specified dataset.  Note: this could be a very large file!
Available options.

 Options:
 -url      The full URL to the dataset
   OR specify a dataset with species, release, and dataset:
 -species  The binomial name or abbreviated form of the species
 -release  The version to fetch
 -dataset  The symbolic name of the dataset (dna, mrna, etc)

This method is a programmatic equivalent to accessing the standard URL:

    http://your.site/genome/Binomial_name/release_name/[dataset]


=item $mod->supported_datasets();

Fetch a list of symbolic names of supported datasets.  This typically
will be a list like "dna", "mrna", "ncrna", "protein", and "feature".

=back

=head1 Standard URL Specification

=head2 PHASE I

Substitutions:

	your.site	Host address, e.g. www.wormbase.org
	Binomial_name	NCBI Taxonomy scientific name, e.g.
			Caenorhabditis_elegans
        release_name    Data release, in whatever is the local
			format (e.g. release date, release number)

=over 4

=item http://your.site/genome/

Leads to index page for species. This should be an HTML-format page
that contains links to each of the species whose genomes are available
for download.

=item http://your.site/genome/Binomial_name/

Leads to index for releases for species Binomial_name. This will be an
HTML-format page containing links to each of the genome releases.

=item http://your.site/genome/Binomial_name/release_name/ 

Leads to index for the named release.  It should be an HTML-format
page containing links to each of the data sets described below.

=item http://your.site/genome/Binomial_name/current/

Leads to the index for the most recent release, symbolic link style.

=item http://your.site/genome/Binomial_name/current/dna

Returns a FASTA file containing big DNA fragments
(e.g. chromosomes). MIME type is application/x-fasta.

=item http://your.site/genome/Binomial_name/current/mrna

Returns a FASTA file containing spliced mRNA transcript
sequences. MIME type is application/x-fasta.

=item http://your.site/genome/Binomial_name/current/ncrna

Returns a FASTA file containing non-coding RNA sequences. MIME type is
application/x-fasta.

=item http://your.site/genome/Binomial_name/current/protein

Returns a FASTA file containing all the protein sequences known to be
encoded by the genome. MIME type is application/x-fasta

=item http://your.site/genome/Binomial_name/current/feature

Returns a GFF3 file describing genome annotations. MIME type is
application/x-gff3.

=back

=head2  PHASE II

In the phase 2 URL scheme, we'll be able to attach ?format=XXXX to
each of the URLs:

=item http://your.site/genome/?format=HTML

    Same as default for phase I.

=item http://your.site/genome/?format=RSS

Return RSS feed indicating what species are available.

=item http://your.site/genome/Binomial_name/?format=RSS
	
Return RSS feed indicating what releases are available.

=item http://your.site/genome/Binomial_name/release_name/?format=RSS
	
Return RSS feed indicating what data sets are available.

=item http://your.site/genome/Binomial_name/current/protein?format=XXX

Alternative formats for sequence data.  E.g. XXX could be FASTA, RAW,
or whatever (for further discussion).

=cut