Question: Document A Ucsc Table Browser Query And/Or Convert Query To An Mysql Expression
1
gravatar for Duarte Molha
6.1 years ago by
Duarte Molha200
Oxford, UK
Duarte Molha200 wrote:

Hi guys

I have been creating some relatively complex UCSC table browser queries and I would like to save the parameters of those queries either as maybe a specific URL or XML web service format, like it is possible in Ensembl Biomart or, even better, a way of converting the query into a mySql expression to programmatically retrieve the same data from UCSC sql server, using my own scripts later on.

Does anyone know if any of this things are possible?

mysql ucsc • 1.6k views
ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by Duarte Molha200

do you use the mysql command line ? you could just pipe a sql file to mysql. Search biostars for "mysql user genome"

ADD REPLYlink written 6.1 years ago by Pierre Lindenbaum122k
1

Sorry Pierre... I know I could just develop the entire query in mySQL... It is just that it is a much more simple and straighforward option to create our query using the table browser... my question was if instead there was a way of retrieving the sql query that is on the backend of the table query since I am almost certain they are exactly one and the same as the one we would construct if I was doing it by the mysql programmatic way. It it clear what I am asking? Sorry I know sometimes I do not explain myself terribly well.

ADD REPLYlink written 6.1 years ago by Duarte Molha200

I see, you cannot get this information using only mysql because the UCSC table browser interacts with things like BAMs, custom tracks etc.. . For a complete answer, you should ask the UCSC mailing list.

ADD REPLYlink written 6.1 years ago by Pierre Lindenbaum122k

Thanks... I'll do that

ADD REPLYlink written 6.1 years ago by Duarte Molha200
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