[Gmod-ajax] UCSC to Jbrowse adaptor

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[Gmod-ajax] UCSC to Jbrowse adaptor

James Morris
Hello,

I saw on the blog that you now have a UCSC to Jbrowse adaptor, this sounds great!

Is this code available to test? I had a look on git hub but could not see anything obvious.

Thanks,

James

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Re: UCSC to Jbrowse adaptor

Mitch Skinner
  There are still a few bugs in it; it's only a few days old, and I
haven't checked it in, yet.  I'll send a message to the list when I do,
probably on Monday or Tuesday.

It currently only supports "bed" and "genePred" tables; psl, bedGraph,
and wiggle tables are still to-do.  I'm not sure how important the other
types (chain, netAlign, ctgPos, expRatio, rmsk, wigMaf) are for JBrowse.

The current version pulls directly from UCSC's public mysql instance;
I'm a little worried that they'll be unhappy with that.  I don't think
it's all that rough on the mysql server, though.  The script spends most
of its time processing the data on the client, and writing out the
JBrowse JSON.  So it's not sending queries terribly frequently.  Some of
the queries it does make can pull out large amounts of data, though.

Mitch

On 10/11/2010 03:00 AM, James Morris wrote:

> Hello,
>
> I saw on the blog that you now have a UCSC to Jbrowse adaptor, this sounds great!
>
> Is this code available to test? I had a look on git hub but could not see anything obvious.
>
> Thanks,
>
> James
>


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experiences on the web. Be a part of the beta today.
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Re: UCSC to Jbrowse adaptor

Mitch Skinner
  I checked in bin/ucsc-to-json.pl on the "jsongen-refactor" branch:

http://github.com/jbrowse/jbrowse/tree/jsongen-refactor

That branch is still very much a work in progress; flatfile-to-json.pl
and biodb-to-json.pl currently don't work on the branch (they do in
master, just not in jsongen-refactor).

There has already been one JSON format change on that branch, and there
will be more; the program names may change, the command line arguments
may change, it's not well documented, etc.  In other words, here be
dragons!  But I said I'd send a message when I checked it in, so here
you go.

The way I've been using it is:

$ rsync -ahvzP --exclude="chain*" --exclude="net*"
rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/
~/data/ucsc/hg19/database

$ bin/ucsc-to-json.pl --in ~/data/ucsc/hg19/database --track "YRI NA18507"

where the --in parameter is the directory with the downloaded annotation
database dumps from UCSC, and the --track parameter is the shortLabel of
the track (the second column in trackDb.txt.gz).

As for whether or not it would be hard to write something for Ensembl, I
really don't know.  Looking at their data is on my to-do list, but I'm
not very familiar with what they provide.

Mitch

On 10/11/2010 04:09 AM, Mitch Skinner wrote:

>  There are still a few bugs in it; it's only a few days old, and I
> haven't checked it in, yet.  I'll send a message to the list when I
> do, probably on Monday or Tuesday.
>
> It currently only supports "bed" and "genePred" tables; psl, bedGraph,
> and wiggle tables are still to-do.  I'm not sure how important the
> other types (chain, netAlign, ctgPos, expRatio, rmsk, wigMaf) are for
> JBrowse.
>
> The current version pulls directly from UCSC's public mysql instance;
> I'm a little worried that they'll be unhappy with that.  I don't think
> it's all that rough on the mysql server, though.  The script spends
> most of its time processing the data on the client, and writing out
> the JBrowse JSON.  So it's not sending queries terribly frequently.  
> Some of the queries it does make can pull out large amounts of data,
> though.
>
> Mitch
>
> On 10/11/2010 03:00 AM, James Morris wrote:
>> Hello,
>>
>> I saw on the blog that you now have a UCSC to Jbrowse adaptor, this
>> sounds great!
>>
>> Is this code available to test? I had a look on git hub but could not
>> see anything obvious.
>>
>> Thanks,
>>
>> James
>>
>


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