diff --git a/.idea/NGS-emulator.iml b/.idea/NGS-emulator.iml
new file mode 100644
index 0000000..7ae5f20
--- /dev/null
+++ b/.idea/NGS-emulator.iml
@@ -0,0 +1,13 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/.idea/libraries/R_User_Library.xml b/.idea/libraries/R_User_Library.xml
new file mode 100644
index 0000000..71f5ff7
--- /dev/null
+++ b/.idea/libraries/R_User_Library.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000..6c993b7
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,4 @@
+
+
+
+
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000..f43dc67
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000..94a25f7
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+
+
+
+
+
+
\ No newline at end of file
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
new file mode 100644
index 0000000..7f9fa45
--- /dev/null
+++ b/.idea/workspace.xml
@@ -0,0 +1,198 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 1513418593515
+
+
+ 1513418593515
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/Cover_emulator.py b/Cover_emulator.py
new file mode 100644
index 0000000..a90b492
--- /dev/null
+++ b/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])
+
+
diff --git a/Emulatior_v0.1.py b/Emulatior_v0.1.py
index d9bdb35..5dcf77c 100644
--- a/Emulatior_v0.1.py
+++ b/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
diff --git a/current_project b/current_project
new file mode 100644
index 0000000..f94bbee
--- /dev/null
+++ b/current_project
@@ -0,0 +1,3 @@
+# current_project
+# start end meanDP
+1 30 10
\ No newline at end of file