Document A Ucsc Table Browser Query And/Or Convert Query To An Mysql Expression

Question

[Duarte Molha]

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?

[Pierre Lindenbaum]

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

[Duarte Molha]

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.

[Pierre Lindenbaum]

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.

[Duarte Molha]

Thanks... I'll do that