...

Author: Dom Laetsch

lib/BtCore.py

@@ -145,7 +145,7 @@ def getPlotData(self, rank, min_length, hide_nohits, taxrule, c_index, catcolour
         data_dict = {}
         read_cov_dict = {}
         max_cov = 0.0
-        
+        print self.covLibs
         cov_lib_dict = self.covLibs
         #print cov_lib_dict
         cov_lib_names_l = self.covLibs.keys() # does not include cov_sum
@@ -203,8 +203,10 @@ def getPlotData(self, rank, min_length, hide_nohits, taxrule, c_index, catcolour
                 cov_sum = 0.0
                 reads_mapped_sum = 0
                 for cov_lib in sorted(cov_lib_names_l):
-                    cov = float(blob['covs'][cov_lib]) 
-                    cov = cov if cov > 0.02 else 0.02
+                    cov = float(blob['covs'][cov_lib])
+                    if cov < 0.02:
+                        cov = 0.02
+                    #cov = cov if cov > 0.02 else 0.02
                     # increase max_cov
                     if cov > max_cov:
                         max_cov = cov
@@ -221,13 +223,13 @@ def getPlotData(self, rank, min_length, hide_nohits, taxrule, c_index, catcolour
                         reads_mapped_sum += reads_mapped
 
                 if len(cov_lib_names_l) > 1:
-                    cov_sum = cov_sum if cov_sum > 0.02 else 0.02
+                    if cov_sum < 0.02 :
+                        cov_sum = 0.02
                     data_dict[group]['covs']['sum'].append(cov_sum)
-                    if cov > max_cov:
-                        max_cov = cov
+                    if cov_sum > max_cov:
+                        max_cov = cov_sum
                     if (reads_mapped_sum):
                         data_dict[group]['reads_mapped']['sum'] += reads_mapped_sum
-
         #if len(cov_lib_names_l) > 1:
         #    for cov_lib, data in self.covLibs.items():
         #        cov_libs_reads_total['cov_sum'] = cov_libs_reads_total.get('cov_sum', 0) + data['reads_total'] 
@@ -312,6 +314,9 @@ def parseCovs(self, covLibObjs):
             else:
                 pass        
             covLib.mean_cov = covLib.cov_sum/self.seqs
+            if covLib.cov_sum == 0.0:
+                print BtLog.error['26'] % (covLib.f)
+            print covLib.cov_sum
             self.covLibs[covLib.name] = covLib
 
 
@@ -377,7 +382,7 @@ def __init__(self, name, fmt, f):
         self.name = name
         self.fmt = fmt
         self.f = abspath(f) if (f) else ''
-        self.cov_sum = 0
+        self.cov_sum = 0.0
         self.reads_total = 0
         self.reads_mapped = 0
         self.mean_cov = 0.0

lib/BtLog.py

@@ -56,7 +56,8 @@ def progress(iteration, steps, max_value):
     '22' : '[ERROR:22]\t: Tax file %s seems to have no taxids.',
     '23' : '[ERROR:23]\t: Catcolour file %s does not seem to have the right format.',
     '24' : '[ERROR:24]\t: Catcolour file incompatible with c-index colouring.',
-    '25' : '[ERROR:25]\t: Cov file %s does not seem to have the right format.'
+    '25' : '[ERROR:25]\t: Cov file %s does not seem to have the right format.',
+    '26' : '[ERROR:26]\t: The cumulative coverage of %s is 0.0. Please check you mapping/coverage file.'
 }
 
 warn_d = {

lib/BtPlot.py

@@ -531,6 +531,7 @@ def plotReadCov(self, refcov_dict):
                 plt.close()            
 
     def plotBlobs(self, cov_lib, info_flag):
+
         rect_scatter, rect_histx, rect_histy, rect_legend = set_canvas()
         # Setting up plots and axes
         plt.figure(1, figsize=(35,35), dpi=400)
@@ -587,12 +588,6 @@ def plotBlobs(self, cov_lib, info_flag):
                 if group == "no-hit":
                     alpha = 0.5
                 weights_array = group_length_array/1000
-                print group
-                print group_gc_array
-                print group_cov_array
-                print weights_array
-                print top_bins
-                print right_bins
                 # generate label for legend
                 fmt_seqs = "{:,}".format(group_number_of_seqs)
                 fmt_span = "{:,}".format(group_span_in_mb)