Fix of merges

Author: DRL

lib/BtCore.py

@@ -57,7 +57,9 @@ def view(self, **kwargs):
         tax_lib_names = [taxLib for taxLib in sorted(self.hitLibs)]
         lineages = self.lineages
         # setup
+
         for viewObj in viewObjs:
+            #print("in view:", viewObj.name)
             if viewObj.name == 'table':
                 viewObj.header = self.getTableHeader(taxrule, ranks, hits_flag, cov_lib_names)
             if viewObj.name == 'concoct_cov':
@@ -100,6 +102,7 @@ def view(self, **kwargs):
                         viewObj.body.append(self.getCovLine(blob, cov_lib_names))
                 pbar.update()
         for viewObj in viewObjs:
+            #print(viewObj.name)
             viewObj.output()
 
     def getCovHeader(self, cov_lib_names):
@@ -763,8 +766,8 @@ def get_meta(self):
         cov_names = filter(lambda name: name != "covsum",self.covs)
         for taxrule in self.tax:
             self.tax_scores[taxrule] = defaultdict(lambda: {'score':[],'c_index':[]})
-        for id in self.blobDb.order_of_blobs:
-            blob = self.blobDb.dict_of_blobs[id]
+        for _id in self.blobDb.order_of_blobs:
+            blob = self.blobDb.dict_of_blobs[_id]
             self.read_covs['covsum'].append(0)
             for cov_name in cov_names:
                 self.read_covs[cov_name].append(blob['read_cov'][cov_name])
@@ -781,11 +784,11 @@ def get_meta(self):
                 cov_libs = []
                 for cov_name in self.covs:
                     name = self._remove_cov_suffix(cov_name,self.blobDb.covLibs)
-                    id = "%s_%s" % (name,cov)
-                    cov_lib_meta = {"id":id, "name":name }
+                    _id = "%s_%s" % (name,cov)
+                    cov_lib_meta = {"id": _id, "name":name }
                     if cov_name == "cov0" and cov == "cov":
                         cov_lib_meta["preload"] = True
-                        meta['plot']['y'] = id
+                        meta['plot']['y'] = _id
                     cov_libs.append(cov_lib_meta)
                 cov_meta = {"id":"%s" % cov, "name":"Coverage", "type":"variable", "datatype":"float", "scale":"scaleLog", "range":self._format_float([0.02,max(self.covs["covsum"])])}
                 if cov == 'read_cov':
@@ -799,14 +802,14 @@ def get_meta(self):
             for taxrule in self.tax:
                 taxrule_meta = {"id":taxrule, "name":taxrule, "children":[] }
                 for rank in self.tax[taxrule]:
-                    id = "%s_%s" % (taxrule,rank)
+                    _id = "%s_%s" % (taxrule,rank)
                     tax_rank_data = []
-                    tax_rank_data.append({ "id":"%s_score" % id, "name":"%s score" % id, "type":"variable", "datatype":"float", "scale":"scaleLog", "range":[0.2,max(self.tax_scores[taxrule][rank]['score'])], "preload":False, "active":False })
-                    tax_rank_data.append({ "id":"%s_cindex" % id, "name":"%s c-index" % id, "type":"variable", "datatype":"integer", "scale":"scaleLinear", "range":[0,max(self.tax_scores[taxrule][rank]['c_index'])], "preload":False, "active":False })
-                    tax_rank_meta = { "id":id, "name":id, "data": tax_rank_data }
+                    tax_rank_data.append({ "id":"%s_score" % _id, "name":"%s score" % _id, "type":"variable", "datatype":"float", "scale":"scaleLog", "range":[0.2,max(self.tax_scores[taxrule][rank]['score'])], "preload":False, "active":False })
+                    tax_rank_data.append({ "id":"%s_cindex" % _id, "name":"%s c-index" % _id, "type":"variable", "datatype":"integer", "scale":"scaleLinear", "range":[0,max(self.tax_scores[taxrule][rank]['c_index'])], "preload":False, "active":False })
+                    tax_rank_meta = { "id":_id, "name":_id, "data": tax_rank_data }
                     if rank == "phylum":
                         tax_rank_meta["preload"] = True
-                        meta['plot']['cat'] = id
+                        meta['plot']['cat'] = _id
                     taxrule_meta['children'].append(tax_rank_meta)
                 tax_rules.append(taxrule_meta)
             tax_meta = {"id":"taxonomy", "name":"Taxonomy", "type":"category", "datatype":"string"}
@@ -833,7 +836,7 @@ def output(self):
         # meta
         meta = self.get_meta()
         meta_f = join(self.view_dir, "meta.json")
-        BtIO.writeJson(meta, meta_f, indent=2)
+        BtIO.writeJson(meta, meta_f)
         # gc
         gc_f = join(self.view_dir, "gc.json")
         print(BtLog.status_d['13'] % (gc_f))

lib/BtIO.py

@@ -585,7 +585,7 @@ def parseNodesDB(**kwargs):
                 BtLog.error('47', nodesDB_f)
             BtLog.status_d['27'] % (nodesDB_f, nodes_f, names_f)
         else:
-            print BtLog.status_d['3'] % (nodes_f, names_f)
+            print(BtLog.status_d['3'] % (nodes_f, names_f))
         try:
             nodesDB = readNamesNodes(names_f, nodes_f)
         except:
@@ -611,11 +611,11 @@ def parseNodesDB(**kwargs):
     # exist.  Otherwise, write to nodesDB_default if it does not exist, unless
     # nodesDB given, then do nothing with nodesDB_default.
     if (nodes_f and names_f and nodesDB_f):
-        print BtLog.status_d['28'] % nodesDB_f
+        print(BtLog.status_d['28'] % nodesDB_f)
         writeNodesDB(nodesDB, nodesDB_f)
     elif (not nodesDB_f and not isfile(nodesDB_default)):
         nodesDB_f = nodesDB_default
-        print BtLog.status_d['5'] % nodesDB_f
+        print(BtLog.status_d['5'] % nodesDB_f)
         writeNodesDB(nodesDB, nodesDB_f)
 
     return nodesDB, nodesDB_f
@@ -744,7 +744,7 @@ def readYaml(infile):
         str = "".join(fh.readlines())
     try:
         data = yaml.load(str)
-    except yaml.YAMLError, exc:
+    except yaml.YAMLError:
         BtLog.error('37', infile, "yaml")
     return data
 

lib/view.py

@@ -92,7 +92,7 @@ def main():
         else:
             tableView = BtCore.ViewObj(name="table", out_f=out_f, suffix="table.txt", body=[])
         viewObjs.append(tableView)
-    if (experimental):
+    if not experimental == 'False':
         meta = {}
         if isfile(experimental):
             meta = BtIO.readYaml(experimental)
@@ -115,6 +115,8 @@ def main():
             covView = BtCore.ViewObj(name="covlib", out_f=out_f, suffix="cov", body=[])
             blobDb.view(viewObjs=[covView], ranks=None, taxrule=None, hits_flag=None, seqs=None, cov_libs=[cov_lib_name], progressbar=True)
     if (viewObjs):
+        #for viewObj in viewObjs:
+        #    print(viewObj.name)
         blobDb.view(viewObjs=viewObjs, ranks=ranks, taxrule=taxrule, hits_flag=hits_flag, seqs=seqs, cov_libs=[], progressbar=True)
     print(BtLog.status_d['19'])