Hello! I'm new to org.biojava.bio.program.das and I have a couple of questions regarding fetching features and sequences from dazzle servers...
At the moment I'm only interested in getting the sequence and annotations from ensembl's database, which should make the problem easier. It's quite obvious when you're browsing http://servlet.sanger.ac.uk:8080/das/ that ensemble got a lot of data. What I'm concerned about is when I look at the different segment sizes <SEGMENT id="21" size="46944323" subparts="yes"/> Some of them are really big. Taking a peek at the demo that follows with biojava-live shows that you are supposed to download the entire sequence and then make operations on it (eg substring). DASSequenceDB dasDB = new DASSequenceDB(dbURL); DASSequence dasSeq = (DASSequence) dasDB.getSequence(seqName); System.out.println("1st 10 bases: " + dasSeq.subStr(1, 10)); Isn't there any way that's more efficient and nicer to the server? Is there any way to throw requests like this: http://servlet.sanger.ac.uk:8080/das/ensembl_Homo_sapiens_core_28_35a/dna?segment=21:1,10 regards Joel _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
