Docs

README.rst

@@ -140,9 +140,9 @@ Configuration File Format
 	####Control Allele Fraction Hotspot####
 	ControlAltFreqHotspot = 0
 	####Case Allele Fraction####
-	CaseAltFreq: 0.08
+	CaseAltFreq: 0.10
 	####Total Case Coverage#####
-	CaseCoverage = 8
+	CaseCoverage = 10
 	####Control Allele Fraction####
 	ControlAltFreq = 0
 	###Overall Supporting Read-pairs ###
@@ -162,13 +162,13 @@ Configuration File Format
 	###Case Supporting splitreads Hotspot ###
 	CaseSupportingSplitReadsHotspot: 0
 	###Control Supporting Read-pairs ###
-	ControlSupportingReads: 5
+	ControlSupportingReads: 3
 	###Control Supporting Read-pairs Hotspot ###
-	ControlSupportingReadsHotspot: 5
+	ControlSupportingReadsHotspot: 3
 	###Control Supporting splitreads ###
-	ControlSupportingSplitReads: 5
+	ControlSupportingSplitReads: 3
 	###Control Supporting splitreads Hotspot ###
-	ControlSupportingSplitReadsHotspot: 5
+	ControlSupportingSplitReadsHotspot: 3
 	###Length of Structural Variant###
 	LengthOfSV: 500
 	###Overall Mapping Quality Threshold###
@@ -232,6 +232,10 @@ Quick Usage
 
 Utilities
 =========
+
+Running iCallSV on MSK-IMPACT Pools
+-----------------------------------
+
 **This is only for MSK-IMPACT internal samples**
 
 .. code-block:: sh
@@ -264,6 +268,28 @@ Utilities
 	  -v, --verbose         make lots of noise [default]
 	  -o /somepath/output, --outDir /somepath/output
 	                        Full Path to the output dir.
+
+
+
+Taking the iCallSV and chechking for processed transcript/cDNA in samples
+-------------------------------------------------------------------------
+
+.. code-block:: sh
 	
+	> python check_cDNA_contamination.py -h
+	usage: check_cDNA_contamination.py [options]
+
+	Calculate cDNA contamination per sample based of the Structural Variants
+	Pipeline result
+
+	optional arguments:
+	  -h, --help            show this help message and exit
+	  -v, --verbose         make lots of noise [default]
+	  -s SVfile.txt, --svFile SVfile.txt
+	                        Location of the structural variant file to be used
+	  -o cDNA_contamination, --outputFileName cDNA_contamination
+	                        Full path name for the output file
+	
+
 	
 	

docs/_build/html/_sources/iCallSV.txt

@@ -57,7 +57,7 @@ This files are given in the ``data`` folder inside iCallSV.
 Configuration File Format
 =========================
 
-.. code-block:: ini
+.. code-block:: sh
 
 	#~~~Template configuration file to run iCallSV~~~#
 	#### Path to python executable ###
@@ -116,9 +116,9 @@ Configuration File Format
 	####Control Allele Fraction Hotspot####
 	ControlAltFreqHotspot = 0
 	####Case Allele Fraction####
-	CaseAltFreq: 0.08
+	CaseAltFreq: 0.10
 	####Total Case Coverage#####
-	CaseCoverage = 8
+	CaseCoverage = 10
 	####Control Allele Fraction####
 	ControlAltFreq = 0
 	###Overall Supporting Read-pairs ###
@@ -138,13 +138,13 @@ Configuration File Format
 	###Case Supporting splitreads Hotspot ###
 	CaseSupportingSplitReadsHotspot: 0
 	###Control Supporting Read-pairs ###
-	ControlSupportingReads: 5
+	ControlSupportingReads: 3
 	###Control Supporting Read-pairs Hotspot ###
-	ControlSupportingReadsHotspot: 5
+	ControlSupportingReadsHotspot: 3
 	###Control Supporting splitreads ###
-	ControlSupportingSplitReads: 5
+	ControlSupportingSplitReads: 3
 	###Control Supporting splitreads Hotspot ###
-	ControlSupportingSplitReadsHotspot: 5
+	ControlSupportingSplitReadsHotspot: 3
 	###Length of Structural Variant###
 	LengthOfSV: 500
 	###Overall Mapping Quality Threshold###
@@ -162,9 +162,10 @@ Quick Usage
 	python iCallSV.py -sc /path/to/template.ini -abam /path/to/casebamFile -bbam /path/to/controlbamFile -aId caseID -bId controlId -o /path/to/output/directory -op prefix_for_the_output_files
 
 
+
 .. code-block:: sh
 
-	> python iCallSV.py -h
+	python iCallSV.py -h
 
 	usage: iCallSV.py [-h] [-v] [-V] -sc config.ini -abam caseBAMFile.bam -bbam
 	                  controlBAMFile.bam -aId caseID -bId controlID -o
@@ -207,11 +208,15 @@ Quick Usage
 
 Utilities
 =========
+
+Running iCallSV on MSK-IMPACT Pools
+-----------------------------------
+
 **This is only for MSK-IMPACT internal samples**
 
 .. code-block:: sh
 
-	> python iCallSV_dmp_wrapper.py -h
+	python iCallSV_dmp_wrapper.py -h
 
 	usage: iCallSV_dmp_wrapper.py [options]
 
@@ -239,11 +244,39 @@ Utilities
 	  -v, --verbose         make lots of noise [default]
 	  -o /somepath/output, --outDir /somepath/output
 	                        Full Path to the output dir.
-
 
+
+
+Taking the iCallSV and chechking for processed transcript/cDNA in samples
+-------------------------------------------------------------------------
+
+.. code-block:: sh
+
+	python check_cDNA_contamination.py -h
+	usage: check_cDNA_contamination.py [options]
+
+	Calculate cDNA contamination per sample based of the Structural Variants
+	Pipeline result
+
+	optional arguments:
+	  -h, --help            show this help message and exit
+	  -v, --verbose         make lots of noise [default]
+	  -s SVfile.txt, --svFile SVfile.txt
+	                        Location of the structural variant file to be used
+	  -o cDNA_contamination, --outputFileName cDNA_contamination
+	                        Full path name for the output file
+
 Submodules
 ==========
 
+iCallSV.iCallSV module
+----------------------
+
+.. automodule:: iCallSV.iCallSV
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 iCallSV.FilterDellyCalls module
 -------------------------------
 
@@ -340,18 +373,19 @@ iCallSV.filterAnnotatedSV module
     :undoc-members:
     :show-inheritance:
 
-iCallSV.iCallSV module
-----------------------
 
-.. automodule:: iCallSV.iCallSV
+iCallSV.utilities.iCallSV_dmp_wrapper module
+--------------------------------------------
+
+.. automodule:: iCallSV.utilities.iCallSV_dmp_wrapper
     :members:
     :undoc-members:
     :show-inheritance:
 
-iCallSV.iCallSV_dmp_wrapper module
-----------------------------------
+iCallSV.utilities.check_cDNA_contamination module
+-------------------------------------------------
 
-.. automodule:: iCallSV.iCallSV_dmp_wrapper
+.. automodule:: iCallSV.utilities.check_cDNA_contamination
     :members:
     :undoc-members:
     :show-inheritance:

docs/_build/html/genindex.html

@@ -129,10 +129,6 @@ <h2 id="G">G</h2>
   <dt><a href="iCallSV.html#iCallSV.FilterDellyCalls.GetFilteredRecords">GetFilteredRecords() (in module iCallSV.FilterDellyCalls)</a>
   </dt>
 
-
-  <dt><a href="iCallSV.html#iCallSV.iCallSV_dmp_wrapper.getSubDirs">getSubDirs() (in module iCallSV.iCallSV_dmp_wrapper)</a>
-  </dt>
-
   </dl></td>
 </tr></table>
 
@@ -180,10 +176,6 @@ <h2 id="I">I</h2>
   </dt>
 
 
-  <dt><a href="iCallSV.html#module-iCallSV.iCallSV_dmp_wrapper">iCallSV.iCallSV_dmp_wrapper (module)</a>
-  </dt>
-
-
   <dt><a href="iCallSV.html#module-iCallSV.launch_FilterDellyCalls">iCallSV.launch_FilterDellyCalls (module)</a>
   </dt>
 
@@ -256,19 +248,15 @@ <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
 
-  <dt><a href="iCallSV.html#iCallSV.iCallSV_dmp_wrapper.main">main() (in module iCallSV.iCallSV_dmp_wrapper)</a>
-  </dt>
-
-
   <dt><a href="iCallSV.html#iCallSV.makebamindex.MakeIndex">MakeIndex() (in module iCallSV.makebamindex)</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
 
   <dt><a href="iCallSV.html#iCallSV.make_analysis_dir.makeOutputDir">makeOutputDir() (in module iCallSV.make_analysis_dir)</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
 
   <dt><a href="iCallSV.html#iCallSV.launchThreads.myThread">myThread (class in iCallSV.launchThreads)</a>
   </dt>
@@ -283,12 +271,6 @@ <h2 id="P">P</h2>
   <dt><a href="iCallSV.html#iCallSV.launchThreads.print_time">print_time() (in module iCallSV.launchThreads)</a>
   </dt>
 
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-
-  <dt><a href="iCallSV.html#iCallSV.iCallSV_dmp_wrapper.processor">processor() (in module iCallSV.iCallSV_dmp_wrapper)</a>
-  </dt>
-
   </dl></td>
 </tr></table>
 
@@ -303,6 +285,8 @@ <h2 id="R">R</h2>
   <dt><a href="iCallSV.html#iCallSV.checkHotSpotList.ReadHotSpotFile">ReadHotSpotFile() (in module iCallSV.checkHotSpotList)</a>
   </dt>
 
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
 
   <dt><a href="iCallSV.html#iCallSV.launchThreads.myThread.run">run() (iCallSV.launchThreads.myThread method)</a>
   </dt>
@@ -342,32 +326,12 @@ <h2 id="R">R</h2>
 
       </dl></dd>
   </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-
-  <dt><a href="iCallSV.html#iCallSV.iCallSV_dmp_wrapper.RunJob">RunJob() (in module iCallSV.iCallSV_dmp_wrapper)</a>
-  </dt>
-
-
-  <dt><a href="iCallSV.html#iCallSV.iCallSV_dmp_wrapper.RunPerPool">RunPerPool() (in module iCallSV.iCallSV_dmp_wrapper)</a>
-  </dt>
-
-  </dl></td>
 </tr></table>
 
 <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%" valign="top"><dl>
 
-  <dt><a href="iCallSV.html#iCallSV.iCallSV_dmp_wrapper.SelectNormal">SelectNormal() (in module iCallSV.iCallSV_dmp_wrapper)</a>
-  </dt>
-
-
-  <dt><a href="iCallSV.html#iCallSV.iCallSV_dmp_wrapper.SetupRun">SetupRun() (in module iCallSV.iCallSV_dmp_wrapper)</a>
-  </dt>
-
-  </dl></td>
-  <td style="width: 33%" valign="top"><dl>
-
   <dt><a href="iCallSV.html#iCallSV.sortbamByCoordinate.sortBam">sortBam() (in module iCallSV.sortbamByCoordinate)</a>
   </dt>