From: Jim Procter Date: Sun, 28 Jun 2015 17:45:34 +0000 (+0100) Subject: JAL-1705 notes about retrieving feature relationships for ensembl loci X-Git-Tag: Release_2_10_0~296^2~90^2~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=58c6b8248851792fa37db90c54d55f419a439cad;p=jalview.git JAL-1705 notes about retrieving feature relationships for ensembl loci --- diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java index b456919..978316b 100644 --- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java +++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java @@ -168,6 +168,20 @@ public class EnsemblSeqProxyTest Assert.assertEquals(sq, DBRefUtils.processQueryToAccessionFor(esq, sq), "Regex for " + esq.getClass().toString() + " not correct."); } + // TODO: + // sequence query with ENSG and anything other than a genomic type will yield + // sequences with different IDs which will + // break the post-processing stage where DBRefs are assigned to sequences. + // -> multiple_sequences = true is needed additional parameter + // http://rest.ensembl.org/sequence/id/ENSG00000157764?content-type=text/x-json;type=protein;multiple_sequences=true + // result with four transcripts, cds, cdna, and protein products. + // * + // features for ENG - + // http://rest.ensembl.org/overlap/id/ENSG00000157764?feature=cds&feature=exon&feature=transcript&content-type=text/x-gff3 + // transcript: gives locus, all transcript products with ENSG parents + // gene: give all ENSG on locus + // exon: all exon boundaries. CDS same info. + // @Test(dataProvider = "ens_seqs", suiteName = "live") // public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq) // throws Exception