Round mean depth for parents allele depth to remove issues with 1.5x mean coverage

noisyplotype.py

@@ -209,7 +209,7 @@ def generate_individuals (nb_individuals, chromosome_size, marker_density, mean_
     #markers_positions = sorted(random.sample(range(chromosome_size),size))
     markers_positions = np.linspace(1, chromosome_size, markers_nb, dtype="int")
 
-    with open('Breakpoints.csv', 'w') as breakpointFile:
+    with open('Breakpoints_3x.csv', 'w') as breakpointFile:
         breakpointFile.write(",".join(["sample","average_bkp_position", "bkp_start_position", "bkp_stop_position", "transitionType"]) + "\n");
         for i in range(nb_individuals):
             print("individual " + str(i+1))
@@ -241,8 +241,8 @@ chromosome_size = 44000000
 cMsize = 180    ## Size of genetic map
 conversion_factor = chromosome_size/cMsize   ## Corresponds to a bpPercM conversion ! Needs to be fixed... Does not produce the correct division!
 marker_density = 0.0055
-mean_depth = 3
-max_depth = 6 #TODO (better estimate of max?)
+mean_depth = 1.5
+max_depth = 3 #TODO (better estimate of max?)
 errA = 0.005
 errB = 0.005
 
@@ -276,7 +276,7 @@ header = [
 
 
 ## Write the VCF files (with and without errors)
-with open('test.vcf', 'w') as file:
+with open('test_3x.vcf', 'w') as file:
     # Write the header of the file
     file.writelines(header)
     
@@ -288,11 +288,11 @@ with open('test.vcf', 'w') as file:
         row = ["chr01", str(markers_positions[m]), ".", "A", "T", ".", ".", ".", "GT:DP:AD:RO:QR:AO:QA:GL"]
         for i in range(0, len(matrix)):
             row.append(matrix[i][m])
-        row.append("0/0:"+ str(mean_depth) + ":" + str(mean_depth) + ",0:.:.:.:.")
-        row.append("1/1:"+ str(mean_depth) + ":0," + str(mean_depth) + ":.:.:.:.")
+        row.append("0/0:"+ str(round(mean_depth)) + ":" + str(round(mean_depth)) + ",0:.:.:.:.")
+        row.append("1/1:"+ str(round(mean_depth)) + ":0," + str(round(mean_depth)) + ":.:.:.:.")
         file.write("\t".join(row) + "\n");
 
-with open('test_error.vcf', 'w') as file:
+with open('test_error_3x.vcf', 'w') as file:
     # Write the header of the file
     file.writelines(header)
     
@@ -304,6 +304,6 @@ with open('test_error.vcf', 'w') as file:
         row = ["chr01", str(markers_positions[m]), ".", "A", "T", ".", ".", ".", "GT:DP:AD:RO:QR:AO:QA:GL"]
         for i in range(0, len(matrix_error)):
             row.append(matrix_error[i][m])
-        row.append("0/0:"+ str(mean_depth) + ":" + str(mean_depth) + ",0:.:.:.:.")
-        row.append("1/1:"+ str(mean_depth) + ":0," + str(mean_depth) + ":.:.:.:.")
+        row.append("0/0:"+ str(round(mean_depth)) + ":" + str(round(mean_depth)) + ",0:.:.:.:.")
+        row.append("1/1:"+ str(round(mean_depth)) + ":0," + str(round(mean_depth)) + ":.:.:.:.")
         file.write("\t".join(row) + "\n");
\ No newline at end of file