Good Morning Blake: What do you mean by "query" ? What are you doing with your BED file ? There are efficient mechanisms to use our data. Let us know what you are doing. If you are attempting to fetch sequence, download the .2bit file for the genome of interest, and use the kent command line tool twoBitToFa. This command binary is available here: ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/ The .2bit files can be found in the /gbdb/ hierarchy, for example: ftp://hgdownload.cse.ucsc.edu/gbdb/hg19/
Or load your bed file as a custom track, use the table browser to extract the sequence of all the features in one operation. -Hiram On 7/3/12 8:30 PM, Blake Allen wrote: > Hi my name is Blake, > > I am a UCSC undergrad doing research. > > I am looking to perform a fairly large batch query using BED format. I have > somewhere in the range of 1000 queries to perform and I was wondering what > are some more efficient ways to access your data? > > > My current process takes approx 5 seconds for each query, and eventually > caused a timeout before I canceled the query. > > Each query is currently sent indiviudually for each sequence. > > Is there a way to query many sequences at once? > > Thank you for your help. > > P.S> I am using Mac OS Lion, using Python urllib2. A BED.txt with about > 1000 different sequence postions on one genome (hg18) and on many > chromosomes. Each sequence approximately 50 bp. > > //B _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
