fixes for gene resolution

Author: hpratt

api/api/data_ws.py

@@ -738,7 +738,7 @@ def _re_detail_linkedGenes(self, j, accession):
 
     def _re_detail_rampage(self, j, accession):
         cre = CRE(self.pgSearch, accession, self.cache)
-        nearbyGenes = cre.nearbyPcGenes()
+        nearbyGenes = self._re_detail_nearbyGenomic(self, accession)[accession]["nearby_genes"]
         nearest = min(nearbyGenes, key=lambda x: x["distance"])
         rampage = Rampage(self.assembly, self.pgSearch, self.cache)
         ret = rampage.getByGene(nearest)

api/api/geneexp_ws.py

@@ -82,11 +82,11 @@ def abort(err):
         r = {"assembly": self.assembly,
              "gene": gene}
         for assay_name in ["total RNA-seq", "polyA RNA-seq", "all"]:
-            single = cge.computeHorBars(name, compartments, biosample_types_selected, assay_name if assay_name != "all" else None)
-            mean = cge.computeHorBarsMean(name, compartments, biosample_types_selected, assay_name if assay_name != "all" else None)
+            single = cge.computeHorBars(gene, compartments, biosample_types_selected, assay_name if assay_name != "all" else None)
+            mean = cge.computeHorBarsMean(gene, compartments, biosample_types_selected, assay_name if assay_name != "all" else None)
             itemsByRID = cge.itemsByRID
             r[assay_name] = {"assembly": self.assembly,
-                             "gene": name,
+                             "gene": gene,
                              "strand": strand,
                              "ensemblid_ver": gi.ensemblid_ver,
                              "coords": {"chrom": gi.chrom,

api/common/pg_parse.py

@@ -65,7 +65,7 @@ def _exactGeneMatch(self, s, usetss, tssDist):
 ac.chrom, ac.start, ac.stop,
 ac.altchrom, ac.altstart, ac.altstop,
 similarity(ac.name, %s) AS sm, ac.pointer,
-gi.approved_symbol, gi.strand
+gi.info->'symbol' AS approved_symbol, gi.strand
 FROM {assembly}_gene_search ac
 INNER JOIN {assembly}_gene_info gi
 ON gi.id = ac.pointer

api/common/pg_search.py

@@ -135,7 +135,7 @@ def crePos(self, accession):
 
     def _getGenes(self, accession, chrom, allOrPc):
         rows = self.pw.fetchall("_getGenes", """
-        SELECT gi.approved_symbol, g.distance, gi.ensemblid_ver, 
+        SELECT gi.info->>'symbol' AS approved_symbol, g.distance, gi.ensemblid_ver, 
         gi.chrom, gi.start, gi.stop
         FROM
         (SELECT UNNEST(gene_{allOrPc}_id) geneid,
@@ -159,8 +159,9 @@ def geneInfo(self, gene):
         WHERE approved_symbol = %s
         OR ensemblid = %s
         OR ensemblid_ver = %s
+        OR info->>'symbol' = %s
         """.format(gtn=self.assembly + "_gene_info"),
-                                          (gene, gene, gene))
+                                          (gene, gene, gene, gene))
         return r
 
     def intersectingSnps(self, accession, coord, halfWindow):
@@ -405,13 +406,14 @@ def genePos(self, gene):
             ensemblid = gene.split('.')[0]
 
         r = self.pw.fetchone("cre_pos", """
-        SELECT chrom, start, stop, approved_symbol, ensemblid_ver FROM {tn}
+        SELECT chrom, start, stop, info->>'symbol' AS approved_symbol, ensemblid_ver FROM {tn}
         WHERE chrom != ''
         AND (approved_symbol = %s
         OR ensemblid = %s
-        OR ensemblid_ver = %s)
+        OR ensemblid_ver = %s
+        OR info->>'symbol' = %s)
         """.format(tn=self.assembly + "_gene_info"),
-                             (gene, ensemblid, gene))
+                             (gene, ensemblid, gene, gene))
         if not r:
             print("ERROR: missing", gene)
             return None, None
@@ -518,15 +520,15 @@ def datasets(self, assay):
 
     def genemap(self):
         rows = self.pw.fetchall("pg::genemap", """
-        SELECT ensemblid, approved_symbol, strand
+        SELECT ensemblid, info->>'symbol' AS approved_symbol, strand
         FROM {tn}
         WHERE strand != ''
         """.format(tn=self.assembly + "_gene_info"))
         toSymbol = {r[0]: r[1] for r in rows}
         toStrand = {r[0]: r[2] for r in rows}
 
         rows = self.pw.fetchall("pg::genemap", """
-        SELECT ensemblid_ver, approved_symbol, strand
+        SELECT ensemblid_ver, info->>'symbol' AS approved_symbol, strand
         FROM {tn}
         WHERE strand != ''
         """.format(tn=self.assembly + "_gene_info"))
@@ -593,9 +595,9 @@ def rampageByGene(self, ensemblid_ver):
         rows = self.pw.fetchallAsDict("rampageByGene", """
         SELECT *
         FROM {tn}
-        WHERE ensemblid_ver = %s
+        WHERE ensemblid_ver ILIKE %s || '%%'
         """.format(tn=self.assembly + "_rampage"),
-                                      (ensemblid_ver, ))
+                                      (ensemblid_ver.split('.')[0], ))
 
         ret = []
         for r in rows:
@@ -624,7 +626,7 @@ def rampageEnsemblID(self, gene):
         r = self.pw.fetchone("rampageEnsemblID", """
         SELECT ensemblid_ver 
         FROM {assembly}_gene_info
-        WHERE approved_symbol = %(gene)s
+        WHERE approved_symbol = %(gene)s OR info->>'symbol' = %(gene)s
         """.format(assembly=self.assembly),
                              {"gene": gene})
         return r[0]
@@ -639,15 +641,15 @@ def geBiosampleTypes(self):
 
     def geneIDsToApprovedSymbol(self):
         rows = self.pw.fetchall("geneIDsToApprovedSymbol", """
-        SELECT geneid, approved_symbol
+        SELECT geneid, info->>'symbol' AS approved_symbol
         FROM {gtn}
         ORDER BY 1
         """.format(gtn=self.assembly + "_gene_info"))
         return {r[0]: r[1] for r in rows}
 
     def genePGIDsToApprovedSymbol(self):
         rows = self.pw.fetchall("geneIDsToApprovedSymbol", """
-        SELECT id, approved_symbol
+        SELECT id, info->>'symbol' AS approved_symbol
         FROM {gtn}
         ORDER BY 1
         """.format(gtn=self.assembly + "_gene_info"))

api/main_apis.py

@@ -217,3 +217,8 @@ def globalData(self, ver, assembly):
     @cherrypy.expose
     def healthz(self):
         return "ok"
+
+    @cherrypy.expose
+    def img(self, *args):
+        cherrypy.response.headers["Content-Type"] = "image/png"
+        return requests.get("http://gcp.wenglab.org/%s" % ('/'.join(args))).content

api/models/cre.py

@@ -70,11 +70,11 @@ def nearbyGenes(self):
         ret.sort(key=lambda g: g["distance"])
         return ret
 
-    def nearbyPcGenes(self):
+    def nearbyPcGenes(self, chromosome = None):
         coord = self.coord()
         if not self.genesAll or not self.genesPC:
             self.genesAll, self.genesPC = self.pgSearch.creGenes(self.accession,
-                                                                 coord.chrom)
+                                                                 chromosome if chromosome is not None else coord.chrom)
         ret = []
         for g in self.genesPC:
             ret.append({"name": g[0], "distance": g[1], "ensemblid_ver": g[2],

api/models/gene_expression.py

@@ -124,7 +124,7 @@ def doComputeHorBars(self, q, gene, compartments, biosample_types_selected,
         a = """
         SELECT chrom, start, stop
         FROM {assembly}_gene_info
-        WHERE approved_symbol = %(gene)s
+        WHERE approved_symbol = %(gene)s OR info->>'symbol' = %(gene)s
         """.format(assembly=self.assembly)
         grows = self.pw.fetchall("doComputeHorBars", a, {"gene": gene})
 

api/server.py

@@ -55,9 +55,7 @@ def getRootConfig(self):
             '/': {
                 'tools.response_headers.on': True,
                 'tools.response_headers.headers': [
-                    ('Access-Control-Allow-Origin', Config.uiURL),
-                    ('Access-Control-Allow-Origin', "https://screen.wenglab.org"),
-                    ('Access-Control-Allow-Origin', "https://screen.encodeproject.org")
+                    ('Access-Control-Allow-Origin', '*')
                 ]
             },
             '/assets': {