Hi, I thought I'd post the answer I got from the archaeal genome browser folks, in case it helps anyone. Apparently, they did change the API slightly and another parameter is necessary, namely:
hgta_track=refSeq So, the whole URL becomes, for example: http://archaea.ucsc.edu/cgi-bin/hgTables ?db=haloHalo1 &hgta_group=allTracks &hgta_track=refSeq &hgta_table=chromInfo &hgta_regionType=genome &hgta_outputType=primaryTable &hgta_doTopSubmit= That works nicely. Thanks, --chris ----- Original Message ---- From: Jennifer Jackson <[email protected]> To: Christopher Bare <[email protected]> Cc: [email protected] Sent: Tue, May 4, 2010 1:47:20 PM Subject: Re: [Genome] programatic access to the archaeal genome browser Hello Christopher, What was formerly called the archaeal browser did undergo some recent changes and we can check with that team if we need to, but first maybe try something simple? The browser is now called "The UCSC Microbial Genome Browser" The server name is now: http://microbes.ucsc.edu If you use the new server name, does this correct the problem? If not please write back and we can go forward from there (check with Todd Lowe's group if necessary). They do handle support (see Credits on server home page) but we also coordinate. If you do reply, please send a few complete url strings (with variables) that do not work now, but used to, for us to test with. If you know when this stopped working, it would also be helpful. Determining if the problem is isolated to one, a few, or all genomes (or a particular phyla/group of phyla) would be good to investigate. Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/4/10 12:22 PM, Christopher Bare wrote: > Hi, > > Are questions related to the archaeal genome browser answered on this list? I > hope so... > > I wrote a desktop program that uses TableBrowser as a data source. I first > ask for the chromInfo table to find the coordinate system of a given genome. > I formerly was able to get this information using a URL constructed like this: > > url = "http://archaea.ucsc.edu/cgi-bin/hgTables?"; + > "db=" + dbName + > "&hgta_group=allTables" + > "&hgta_table=chromInfo" + > "&hgta_regionType=genome" + > "&hgta_outputType=primaryTable" + > "&hgta_doTopSubmit="; > > > It seems that something has changed on the back end, and this no longer > works. Could someone please point me in the right direction to retrieve this > data? > > Any hints are greatly appreciated, Thanks, > > - chris > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
