From 59b9a08633f6e0ef7573f98a228ed736b39ee46d Mon Sep 17 00:00:00 2001
From: AlexanderKononov <kononov.nov@mail.ru>
Date: Wed, 20 Dec 2017 15:57:17 +0200
Subject: [PATCH] add simulation of normal sampl and pycharm file

---
 .idea/NGS-emulator.iml             |  13 ++
 .idea/libraries/R_User_Library.xml |   6 +
 .idea/misc.xml                     |   4 +
 .idea/modules.xml                  |   8 ++
 .idea/vcs.xml                      |   6 +
 .idea/workspace.xml                | 198 +++++++++++++++++++++++++++++
 Cover_emulator.py                  |  29 +++++
 Emulatior_v0.1.py                  |  27 ++--
 current_project                    |   3 +
 9 files changed, 284 insertions(+), 10 deletions(-)
 create mode 100644 .idea/NGS-emulator.iml
 create mode 100644 .idea/libraries/R_User_Library.xml
 create mode 100644 .idea/misc.xml
 create mode 100644 .idea/modules.xml
 create mode 100644 .idea/vcs.xml
 create mode 100644 .idea/workspace.xml
 create mode 100644 Cover_emulator.py
 create mode 100644 current_project

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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="Python 3.5" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" name="R Skeletons" level="application" />
+    <orderEntry type="library" name="R User Library" level="project" />
+  </component>
+  <component name="TestRunnerService">
+    <option name="PROJECT_TEST_RUNNER" value="Unittests" />
+  </component>
+</module>
\ 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 @@
+<component name="libraryTable">
+  <library name="R User Library">
+    <CLASSES />
+    <SOURCES />
+  </library>
+</component>
\ 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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.5" project-jdk-type="Python SDK" />
+</project>
\ 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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/NGS-emulator.iml" filepath="$PROJECT_DIR$/.idea/NGS-emulator.iml" />
+    </modules>
+  </component>
+</project>
\ 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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
\ 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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ChangeListManager">
+    <list default="true" id="d85180b2-f810-4718-a579-984a1e4d4b08" name="Default" comment="">
+      <change beforePath="" afterPath="$PROJECT_DIR$/.idea/libraries/R_User_Library.xml" />
+      <change beforePath="" afterPath="$PROJECT_DIR$/.idea/vcs.xml" />
+      <change beforePath="" afterPath="$PROJECT_DIR$/Cover_emulator.py" />
+      <change beforePath="$PROJECT_DIR$/Emulatior_v0.1.py" afterPath="$PROJECT_DIR$/Emulatior_v0.1.py" />
+    </list>
+    <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" />
+    <option name="TRACKING_ENABLED" value="true" />
+    <option name="SHOW_DIALOG" value="false" />
+    <option name="HIGHLIGHT_CONFLICTS" value="true" />
+    <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
+    <option name="LAST_RESOLUTION" value="IGNORE" />
+  </component>
+  <component name="FileEditorManager">
+    <leaf SIDE_TABS_SIZE_LIMIT_KEY="300">
+      <file leaf-file-name="Cover_emulator.py" pinned="false" current-in-tab="true">
+        <entry file="file://$PROJECT_DIR$/Cover_emulator.py">
+          <provider selected="true" editor-type-id="text-editor">
+            <state relative-caret-position="390">
+              <caret line="26" column="59" lean-forward="false" selection-start-line="26" selection-start-column="59" selection-end-line="26" selection-end-column="59" />
+              <folding />
+            </state>
+          </provider>
+        </entry>
+      </file>
+    </leaf>
+  </component>
+  <component name="FileTemplateManagerImpl">
+    <option name="RECENT_TEMPLATES">
+      <list>
+        <option value="Python Script" />
+      </list>
+    </option>
+  </component>
+  <component name="Git.Settings">
+    <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
+  </component>
+  <component name="IdeDocumentHistory">
+    <option name="CHANGED_PATHS">
+      <list>
+        <option value="$PROJECT_DIR$/Cover_emulator.py" />
+      </list>
+    </option>
+  </component>
+  <component name="ProjectFrameBounds">
+    <option name="x" value="312" />
+    <option name="y" value="56" />
+    <option name="width" value="1308" />
+    <option name="height" value="939" />
+  </component>
+  <component name="ProjectView">
+    <navigator currentView="ProjectPane" proportions="" version="1">
+      <flattenPackages />
+      <showMembers />
+      <showModules />
+      <showLibraryContents />
+      <hideEmptyPackages />
+      <abbreviatePackageNames />
+      <autoscrollToSource />
+      <autoscrollFromSource />
+      <sortByType />
+      <manualOrder />
+      <foldersAlwaysOnTop value="true" />
+    </navigator>
+    <panes>
+      <pane id="Scratches" />
+      <pane id="Scope" />
+      <pane id="ProjectPane">
+        <subPane>
+          <expand>
+            <path>
+              <item name="NGS-emulator" type="b2602c69:ProjectViewProjectNode" />
+              <item name="NGS-emulator" type="462c0819:PsiDirectoryNode" />
+            </path>
+          </expand>
+          <select />
+        </subPane>
+      </pane>
+    </panes>
+  </component>
+  <component name="PropertiesComponent">
+    <property name="settings.editor.selected.configurable" value="project.propVCSSupport.Mappings" />
+  </component>
+  <component name="RunDashboard">
+    <option name="ruleStates">
+      <list>
+        <RuleState>
+          <option name="name" value="ConfigurationTypeDashboardGroupingRule" />
+        </RuleState>
+        <RuleState>
+          <option name="name" value="StatusDashboardGroupingRule" />
+        </RuleState>
+      </list>
+    </option>
+  </component>
+  <component name="RunManager">
+    <configuration name="Cover_emulator" type="PythonConfigurationType" factoryName="Python" temporary="true">
+      <option name="INTERPRETER_OPTIONS" value="" />
+      <option name="PARENT_ENVS" value="true" />
+      <envs>
+        <env name="PYTHONUNBUFFERED" value="1" />
+      </envs>
+      <option name="SDK_HOME" value="/usr/bin/python3.5" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
+      <option name="IS_MODULE_SDK" value="false" />
+      <option name="ADD_CONTENT_ROOTS" value="true" />
+      <option name="ADD_SOURCE_ROOTS" value="true" />
+      <module name="NGS-emulator" />
+      <option name="SCRIPT_NAME" value="$PROJECT_DIR$/Cover_emulator.py" />
+      <option name="PARAMETERS" value="-normal 30 10" />
+      <option name="SHOW_COMMAND_LINE" value="false" />
+      <option name="EMULATE_TERMINAL" value="false" />
+      <option name="MODULE_MODE" value="false" />
+    </configuration>
+    <recent_temporary>
+      <list size="1">
+        <item index="0" class="java.lang.String" itemvalue="Python.Cover_emulator" />
+      </list>
+    </recent_temporary>
+  </component>
+  <component name="ShelveChangesManager" show_recycled="false">
+    <option name="remove_strategy" value="false" />
+  </component>
+  <component name="SvnConfiguration">
+    <configuration />
+  </component>
+  <component name="TaskManager">
+    <task active="true" id="Default" summary="Default task">
+      <changelist id="d85180b2-f810-4718-a579-984a1e4d4b08" name="Default" comment="" />
+      <created>1513418593515</created>
+      <option name="number" value="Default" />
+      <option name="presentableId" value="Default" />
+      <updated>1513418593515</updated>
+    </task>
+    <servers />
+  </component>
+  <component name="ToolWindowManager">
+    <frame x="312" y="56" width="1308" height="939" extended-state="0" />
+    <editor active="true" />
+    <layout>
+      <window_info id="Project" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.26875958" sideWeight="0.5" order="0" side_tool="false" content_ui="combo" />
+      <window_info id="TODO" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="6" side_tool="false" content_ui="tabs" />
+      <window_info id="R Packages" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="R Graphics" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="Event Log" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="7" side_tool="true" content_ui="tabs" />
+      <window_info id="Run" active="true" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="true" show_stripe_button="true" weight="0.3293556" sideWeight="0.5" order="2" side_tool="false" content_ui="tabs" />
+      <window_info id="Version Control" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
+      <window_info id="Python Console" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
+      <window_info id="Structure" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
+      <window_info id="Terminal" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="7" side_tool="false" content_ui="tabs" />
+      <window_info id="Debug" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.4" sideWeight="0.5" order="3" side_tool="false" content_ui="tabs" />
+      <window_info id="Favorites" active="false" anchor="left" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="2" side_tool="true" content_ui="tabs" />
+      <window_info id="Cvs" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="4" side_tool="false" content_ui="tabs" />
+      <window_info id="Message" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="0" side_tool="false" content_ui="tabs" />
+      <window_info id="Commander" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.4" sideWeight="0.5" order="0" side_tool="false" content_ui="tabs" />
+      <window_info id="Inspection" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.4" sideWeight="0.5" order="5" side_tool="false" content_ui="tabs" />
+      <window_info id="Hierarchy" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="2" side_tool="false" content_ui="combo" />
+      <window_info id="Find" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
+      <window_info id="Ant Build" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" />
+    </layout>
+  </component>
+  <component name="VcsContentAnnotationSettings">
+    <option name="myLimit" value="2678400000" />
+  </component>
+  <component name="XDebuggerManager">
+    <breakpoint-manager />
+    <watches-manager />
+  </component>
+  <component name="editorHistoryManager">
+    <entry file="file://$PROJECT_DIR$/Cover_emulator.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="0">
+          <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/current_project">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="0">
+          <caret line="0" column="0" lean-forward="false" selection-start-line="0" selection-start-column="0" selection-end-line="0" selection-end-column="0" />
+          <folding />
+        </state>
+      </provider>
+    </entry>
+    <entry file="file://$PROJECT_DIR$/Cover_emulator.py">
+      <provider selected="true" editor-type-id="text-editor">
+        <state relative-caret-position="390">
+          <caret line="26" column="59" lean-forward="false" selection-start-line="26" selection-start-column="59" selection-end-line="26" selection-end-column="59" />
+          <folding />
+        </state>
+      </provider>
+    </entry>
+  </component>
+</project>
\ 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