[DAS2] [Bug 1807] New: Where do seqids come from?

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1807

           Summary: Where do seqids come from?
           Product: BioDAS
           Version: 2
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Spec - GET Requests
        AssignedTo: das2 at portal.open-bio.org
        ReportedBy: dalke at dalkescientific.com


Did a stork drop them off in the cabbage patch?

I'm trying to understand regions and their relationship to sequence.

The spec says

> seqid is the sequence ID, and can correspond to an assembled chromosome, a
> contig, a clone, or any other accessionable chunk of sequence

Is the seqid exactly equivalent to a region id?

I think so given the documentation in das2_protocol.html.

The das2_protocol.html document also says

> http://server/das/genome/sourceid/version/region/regionid/subregion
> A genomic region region identified by the ID of a landmark, modified by
> a subregion relative to the landmark. As a whole, the URL is a globally
> unique identifier for a region of the genome.
>
> The syntax of addressing regions and subregions is described in detail later.

The das2_get.html document says

> Adding a subregion restricts the document further to regions that overlap the indicated subregion.
> 
> REQUEST:
>
>    GET http://server/das/genome/sourceid/version/region/ctg2
> or
>    GET http://server/das/genome/sourceid/version/region/ctg2/34/128

What are the '24' and '128'?  Are they coordinate ranges?  Are they independently
accessionable chunks of the genome, so that

   .../sequence/34?format=fasta

is valid?  Or do I get the sequence via

   .../sequence/ctg2/34/?format=fasta



------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.