add simulation of normal sampl and pycharm file

Cover_emulator.py

@@ -0,0 +1,29 @@
+#This script run with 3 arguments first is comand '-normal',
+# second is lengh of DNA data
+# and third is mean resd depth of normal sample.
+#Then script create template for data with 3 chromosome  and with noted summery DNA lengh and mean read depth.
+
+import sys
+
+def createNormalTemplate(simulation, DNAlengh, meanDP):
+    project_file=open(simulation, 'w')
+    project_file.write('# '+simulation+'\n# start\tend\tmeanDP\n')
+    project_file.write(str(1)+'\t'+str(DNAlengh)+'\t'+str(meanDP))
+    project_file.close()
+
+def test_createNormalTemplate():
+    createNormalTemplate('test_createNormalTemplate', 20, 10)
+    test_file=open('test_createNormalTemplate', 'r')
+    for i in test_file:
+        if i[0]!='#':
+            result = i.strip().split()
+    assert result[0] == '1'
+    assert result[1] == '20'
+    assert result[2] == '10'
+
+arg=sys.argv
+
+if arg[1]=='-normal':
+    createNormalTemplate('current_project', arg[2], arg[3])
+
+

Emulatior_v0.1.py

@@ -1,18 +1,25 @@
-
-# coding: utf-8
-
-# In[16]:
-
 import numpy as np
 import random
 import copy
+import sys
 
-#N_observ=10
-#N_subclones=2
-N_observ=int(raw_input('Size of emulated data?'))
-N_subclones=int(raw_input('Number of emulated subclones?'))
-norm_data=np.zeros((N_observ,4))
+N_observations=100
+N_subclones=2
+exprestion=20
+non-abberant_cells=0.2
+#N_observ=int(raw_input('Size of emulated data?'))
+#N_subclones=int(raw_input('Number of emulated subclones?'))
+norm_data=np.zeros((N_observations,4))
 
+change_frame=N_observations/(N_subclones+2)
+
+normal_CNA=np.random.poisson(exprestion, N_observations)
+subclon_CNA_data={}
+for i in range(N_subclones):
+	current_subclone_data=normal_CNA
+	current_subclone_data[j]+=i*exprestion for j in range(i*change_frame,(i+1)*change_frame)		
+
+	subclon_CNA_data[1]=[]
 # DP Emulate
 for i in norm_data:
     i[0]=1

current_project

@@ -0,0 +1,3 @@
+# current_project
+# start	end	meanDP
+1	30	10