From fff169e7f30cb2e21717fd79d5fb0f80bb37ee1c Mon Sep 17 00:00:00 2001 From: Ronak H Shah Date: Tue, 7 Jun 2016 09:31:08 -0400 Subject: [PATCH] Docs --- README.rst | 38 +- docs/_build/doctrees/environment.pickle | Bin 164804 -> 164664 bytes docs/_build/doctrees/iCallSV.doctree | Bin 361190 -> 328225 bytes docs/_build/html/_sources/iCallSV.txt | 66 ++- docs/_build/html/genindex.html | 44 +- docs/_build/html/iCallSV.html | 386 ++++++------------ docs/_build/html/index.html | 20 +- docs/_build/html/objects.inv | Bin 803 -> 734 bytes docs/_build/html/py-modindex.html | 5 - docs/_build/html/searchindex.js | 2 +- docs/_build/json/_sources/iCallSV.txt | 66 ++- docs/_build/json/environment.pickle | Bin 164804 -> 164664 bytes docs/_build/json/genindex.fjson | 2 +- docs/_build/json/iCallSV.fjson | 2 +- docs/_build/json/index.fjson | 2 +- docs/_build/json/objects.inv | Bin 798 -> 727 bytes docs/_build/json/py-modindex.fjson | 2 +- docs/_build/json/searchindex.json | 2 +- docs/_build/latex/iCallSV.tex | 376 +++++------------ docs/iCallSV.rst | 66 ++- iCallSV/configuration/template.ini | 31 +- iCallSV/utilities/check_cDNA_contamination.py | 116 ++++++ .../{ => utilities}/iCallSV_dmp_wrapper.py | 0 23 files changed, 571 insertions(+), 655 deletions(-) create mode 100755 iCallSV/utilities/check_cDNA_contamination.py rename iCallSV/{ => utilities}/iCallSV_dmp_wrapper.py (100%) diff --git a/README.rst b/README.rst index 2f5bf0c..7be8361 100644 --- a/README.rst +++ b/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 + + \ No newline at end of file diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle index 1ff1efe85ee27b97fccd28fa0e61a51336a47898..02a4a53c6abae12fe45273283dbf3f45b89634a1 100644 GIT binary patch delta 26191 zcmbVVcVH7o_C^b?7+kQ8jV&+&gDEy0l0YEz5C;;<5~VmsmIbn~CGSY0By0r9;e_-= zmu$+V_g+W>X@vCN+vU=8m)xaXF6H{A{J!^QM;4MClixq{=FQCa-pn^|cV|cI@e`-! 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z>{P>C_F*Pb#c|1SI-pj$Y(`?bBHYs^yDzdbUXu+0^Y!iiUtCCB4IWiu8ZVoB$gbN)ny(Mh;Lt)&-p9D-LAOZ9xewP1mzoM4maiDrin`PI_}xzpkIzltMIO&DC91rSl{_&ei7Z{jPrt} qIK1qJ*7%E^eA^)?E!+jm+Fms6w7Ze2mI*Ja_TWdq-HQ~mX8!}3!1yfy diff --git a/docs/_build/html/_sources/iCallSV.txt b/docs/_build/html/_sources/iCallSV.txt index 210668a..8b8d8a8 100644 --- a/docs/_build/html/_sources/iCallSV.txt +++ b/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: diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html index 0b34eb9..32b9187 100644 --- a/docs/_build/html/genindex.html +++ b/docs/_build/html/genindex.html @@ -129,10 +129,6 @@

G

GetFilteredRecords() (in module iCallSV.FilterDellyCalls)
- -
getSubDirs() (in module iCallSV.iCallSV_dmp_wrapper) -
- @@ -180,10 +176,6 @@

I

-
iCallSV.iCallSV_dmp_wrapper (module) -
- -
iCallSV.launch_FilterDellyCalls (module)
@@ -256,19 +248,15 @@

M

- + -
-
main() (in module iCallSV.iCallSV_dmp_wrapper) -
- -
MakeIndex() (in module iCallSV.makebamindex)
-
makeOutputDir() (in module iCallSV.make_analysis_dir)
+
myThread (class in iCallSV.launchThreads)
@@ -283,12 +271,6 @@

P

print_time() (in module iCallSV.launchThreads)
-
- -
processor() (in module iCallSV.iCallSV_dmp_wrapper) -
-
@@ -303,6 +285,8 @@

R

ReadHotSpotFile() (in module iCallSV.checkHotSpotList)
+ +
run() (iCallSV.launchThreads.myThread method)
@@ -342,32 +326,12 @@

R

-
- -
RunJob() (in module iCallSV.iCallSV_dmp_wrapper) -
- - -
RunPerPool() (in module iCallSV.iCallSV_dmp_wrapper) -
- -

S

- - - -
-
SelectNormal() (in module iCallSV.iCallSV_dmp_wrapper) -
- - -
SetupRun() (in module iCallSV.iCallSV_dmp_wrapper) -
- -
-
sortBam() (in module iCallSV.sortbamByCoordinate)
diff --git a/docs/_build/html/iCallSV.html b/docs/_build/html/iCallSV.html index 0954e4d..bdb359e 100644 --- a/docs/_build/html/iCallSV.html +++ b/docs/_build/html/iCallSV.html @@ -141,38 +141,38 @@

Required Data Files

Configuration File Format¶

-
#~~~Template configuration file to run iCallSV~~~#
-#### Path to python executable ###
-[Python]
+
#~~~Template configuration file to run iCallSV~~~#
+#### Path to python executable ###
+[Python]
 PYTHON:
-#### Path to R executable and R Lib ###
-[R]
+#### Path to R executable and R Lib ###
+[R]
 RHOME:
 RLIB:
-#### Path to delly, bcftools executables and Version of delly (supports only 0.7.3)###
-[SVcaller]
+#### Path to delly, bcftools executables and Version of delly (supports only 0.7.3)###
+[SVcaller]
 DELLY:
 DellyVersion:
 BCFTOOLS:
-#### Path to hg19 Referece Fasta file ###
-[ReferenceFasta]
+#### Path to hg19 Referece Fasta file ###
+[ReferenceFasta]
 REFFASTA:
-#### Path to file containing regions to exclude please follow Delly documentation for this ###
-[ExcludeRegion]
+#### Path to file containing regions to exclude please follow Delly documentation for this ###
+[ExcludeRegion]
 EXREGIONS:
-#### Path to file containing regions to where lenient threshold will be used; and file containing genes to keep ###
-[HotSpotRegions]
+#### Path to file containing regions to where lenient threshold will be used; and file containing genes to keep ###
+[HotSpotRegions]
 HotspotFile:
 GenesToKeep:
-#### Path to file containing regions/genes to filter ###
-[BlackListRegions]
+#### Path to file containing regions/genes to filter ###
+[BlackListRegions]
 BlackListFile:
 BlackListGenes:
-#### Path to samtools executable ###
-[SAMTOOLS]
+#### Path to samtools executable ###
+[SAMTOOLS]
 SAMTOOLS:
-#### Path to iAnnotateSV.py and all its required files, please follow iAnnotateSV documentation ###
-[iAnnotateSV]
+#### Path to iAnnotateSV.py and all its required files, please follow iAnnotateSV documentation ###
+[iAnnotateSV]
 ANNOSV:
 GENOMEBUILD:
 DISTANCE:
@@ -181,57 +181,57 @@ 
Configuration File Format#### TargetSeqView Parameters ###
+[TargetSeqView]
 CalculateConfidenceScore:
 GENOMEBUILD:
 ReadLength:
-#### Parameters to run Delly ###
-[ParametersToRunDelly]
+#### Parameters to run Delly ###
+[ParametersToRunDelly]
 MAPQ: 20
 NumberOfProcessors: 4
-[ParametersToFilterDellyResults]
-####Case Allele Fraction Hotspot####
+[ParametersToFilterDellyResults]
+####Case Allele Fraction Hotspot####
 CaseAltFreqHotspot: 0.05
-####Total Case Coverage Hotspot#####
-CaseCoverageHotspot = 5
-####Control Allele Fraction Hotspot####
-ControlAltFreqHotspot = 0
-####Case Allele Fraction####
-CaseAltFreq: 0.08
-####Total Case Coverage#####
-CaseCoverage = 8
-####Control Allele Fraction####
-ControlAltFreq = 0
-###Overall Supporting Read-pairs ###
+####Total Case Coverage Hotspot#####
+CaseCoverageHotspot = 5
+####Control Allele Fraction Hotspot####
+ControlAltFreqHotspot = 0
+####Case Allele Fraction####
+CaseAltFreq: 0.10
+####Total Case Coverage#####
+CaseCoverage = 10
+####Control Allele Fraction####
+ControlAltFreq = 0
+###Overall Supporting Read-pairs ###
 OverallSupportingReads: 5
-###Overall Supporting Read-pairs Hotspot ###
+###Overall Supporting Read-pairs Hotspot ###
 OverallSupportingReadsHotspot: 3
-###Overall Supporting splitreads ###
+###Overall Supporting splitreads ###
 OverallSupportingSplitReads: 0
-###Overall Supporting splitreads Hotspot ###
+###Overall Supporting splitreads Hotspot ###
 OverallSupportingSplitReadsHotspot: 0
-###Case Supporting Read-pairs ###
+###Case Supporting Read-pairs ###
 CaseSupportingReads: 2
-###Case Supporting splitreads ###
+###Case Supporting splitreads ###
 CaseSupportingSplitReads: 0
-###Case Supporting Read-pairs Hotspot ###
+###Case Supporting Read-pairs Hotspot ###
 CaseSupportingReadsHotspot: 1
-###Case Supporting splitreads Hotspot ###
+###Case Supporting splitreads Hotspot ###
 CaseSupportingSplitReadsHotspot: 0
-###Control Supporting Read-pairs ###
-ControlSupportingReads: 5
-###Control Supporting Read-pairs Hotspot ###
-ControlSupportingReadsHotspot: 5
-###Control Supporting splitreads ###
-ControlSupportingSplitReads: 5
-###Control Supporting splitreads Hotspot ###
-ControlSupportingSplitReadsHotspot: 5
-###Length of Structural Variant###
+###Control Supporting Read-pairs ###
+ControlSupportingReads: 3
+###Control Supporting Read-pairs Hotspot ###
+ControlSupportingReadsHotspot: 3
+###Control Supporting splitreads ###
+ControlSupportingSplitReads: 3
+###Control Supporting splitreads Hotspot ###
+ControlSupportingSplitReadsHotspot: 3
+###Length of Structural Variant###
 LengthOfSV: 500
-###Overall Mapping Quality Threshold###
+###Overall Mapping Quality Threshold###
 OverallMapq: 20
-###Overall Mapping Quality Threshold Hotspot###
+###Overall Mapping Quality Threshold Hotspot###
 OverallMapqHotspot: 5
 

 

@@ -241,7 +241,7 @@ 
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
-
> 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
@@ -286,8 +286,10 @@ 
Quick Usage
 
Utilities¶

+

+
Running iCallSV on MSK-IMPACT Pools¶

 
This is only for MSK-IMPACT internal samples

-
> python iCallSV_dmp_wrapper.py -h
+
python iCallSV_dmp_wrapper.py -h
 
 usage: iCallSV_dmp_wrapper.py [options]
 
@@ -318,8 +320,56 @@ 
Utilities
+
Taking the iCallSV and chechking for processed transcript/cDNA in samples¶

+
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¶

+

+
iCallSV¶

+
+++
+
+
+
+
+
+
+
+
+
+
+
+



Description:
iCallSV is a wrapper to the iCallSV package which facilitates calling structural variants from Next Generation Sequencing methods such as Illumina

+
author:
Ronak H Shah

+
copyright:
    
+
  1. 2015-2016 by Ronak H Shah for Memorial Sloan Kettering Cancer Center. All rights reserved.
    2. 
+

+
license:
Apache License 2.0

+
contact:
rons.shah@gmail.com

+

+

+

 

 
iCallSV.FilterDellyCalls module¶

 

@@ -1078,207 +1128,11 @@ 
filterAnnotatedSV
-
iCallSV.iCallSV module¶

-

-
iCallSV¶

-
---
-
-
-
-
-
-
-
-
-
-
-
-



Description:
iCallSV is a wrapper to the iCallSV package which facilitates calling structural variants from Next Generation Sequencing methods such as Illumina

-
author:
Ronak H Shah

-
copyright:
    
-
  1. 2015-2016 by Ronak H Shah for Memorial Sloan Kettering Cancer Center. All rights reserved.
    2. 
-

-
license:
Apache License 2.0

-
contact:
rons.shah@gmail.com

-

-

-

-

-
iCallSV.iCallSV_dmp_wrapper module¶

-

-
iCallSV_dmp_wrapper¶

-
---
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-



Description:
iCallSV is a wrapper to run the iCallSV package on MSKCC data

-
author:
Ronak H Shah

-
copyright:
    
-
  1. 2015-2016 by Ronak H Shah for Memorial Sloan Kettering Cancer Center. All rights reserved.
    2. 
-

-
license:
Apache License 2.0

-
contact:
rons.shah@gmail.com

-
deffield    updated:
 
Updated

-

-

-

-iCallSV.iCallSV_dmp_wrapper.RunJob(cmd)[source]¶

-
Given a command run the job.

-
---
-
-
-
-
-
-
-
-



Parameters:cmd (str) – str of command to be run on the local machine
Returns:None
Return type:None

-

-
-

-

-iCallSV.iCallSV_dmp_wrapper.RunPerPool(titleFile, outdir, HSmetricsFileList, bamFileList, args)[source]¶

-
This will run the pool to be analyzed.

-
---
-
-
-
-
-
-
-
-



Parameters:
    
-
  • titleFile (str) – str of meta information file
    • 
-
  • outdir (str) – str of output directory
    • 
-
  • HSmetricsFileList (list) – list of picard hsmetrics files
    • 
-
  • bamFileList (list) – list of bam files
    • 
-
  • args (Namespace) – Namespace of args to get other variables
    • 
-

-
Returns:
None

-
Return type:
None

-

-

-
-

-

-iCallSV.iCallSV_dmp_wrapper.SelectNormal(normal, poolnormal)[source]¶

-
Select the best possible normal.

-
---
-
-
-
-
-
-
-
-



Parameters:
    
-
  • normal (str) – str of match normal
    • 
-
  • poolnormal (str) – str of pool normal
    • 
-

-
Returns:
str with decision whether to run matched or unmatched

-
Return type:
str

-

-

-
-

-

-iCallSV.iCallSV_dmp_wrapper.SetupRun(poolName, args)[source]¶

-
This will setup the run to be analyzed.

-
---
-
-
-
-
-
-
-
-



Parameters:
    
-
  • poolName (str) – str of pool to be analyzed
    • 
-
  • args (Namespace) – Namespace of args to get other variables
    • 
-

-
Returns:
Multiple objects

-
Return type:
list

-

-

-
-

-

-iCallSV.iCallSV_dmp_wrapper.getSubDirs(dirLocation)[source]¶

-
Get all sub directories.

-
---
-
-
-
-
-
-
-
-



Parameters:dirLocation (str) – str of directory location
Returns:list of all sub directories
Return type:list

-

-
-

-

-iCallSV.iCallSV_dmp_wrapper.main()[source]¶

-

-
-

-

-iCallSV.iCallSV_dmp_wrapper.processor(i, jobqueue)[source]¶

-
Operate on a jobqueue.

-
---
-
-
-
-
-
-
-
-



Parameters:
    
-
  • i (int) – count of the job
    • 
-
  • jobqueue (Namespace) – Namespace for jobqueue
    • 
-

-
Returns:
None

-
Return type:
None

-

-

-
+

+
iCallSV.utilities.iCallSV_dmp_wrapper module¶

 

+

+
iCallSV.utilities.check_cDNA_contamination module¶

 

 

 
iCallSV.launchThreads module¶

@@ -1547,8 +1401,16 @@ 
Table Of Contents

 
  • Required Data Files
    • 
 
  • Configuration File Format
    • 
 
  • Quick Usage
    • 
-
  • Utilities
    • 
+
  • Utilities
+
    • 
 
  • Submodules
 
    • 
-
  • iCallSV.iCallSV module
-
    • 
-
  • iCallSV.iCallSV_dmp_wrapper module
-
    • 
+
  • iCallSV.utilities.iCallSV_dmp_wrapper module
    • 
+
  • iCallSV.utilities.check_cDNA_contamination module
    • 
 
  • iCallSV.launchThreads module
    • 
 
  • iCallSV.launch_FilterDellyCalls module

    		•     iCallSV.iCallSV
        - iCallSV.iCallSV_dmp_wrapper -
        diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js index aa3553c..1dd2aa7 100644 --- a/docs/_build/html/searchindex.js +++ b/docs/_build/html/searchindex.js @@ -1 +1 @@ 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Structural Aberration Detection from NGS datasets","iCallSV: Structural Aberration Detection from NGS datasets"],titleterms:{aberr:[0,1],cdna:0,chechk:0,check_cdna_contamin:0,checkblacklist:0,checkhotspotlist:0,checkparamet:0,citat:1,combinevcf:0,configur:0,content:0,data:0,dataset:[0,1],dellyvcf2tab:0,dellyvcf2targetseqview:0,detect:[0,1],file:0,filterannotatedsv:0,filterdellycal:0,format:0,from:[0,1],icallsv:[0,1],icallsv_dmp_wrapp:0,impact:0,indic:1,launch_filterdellycal:0,launch_run_delli:0,launchthread:0,make_analysis_dir:0,makebamindex:0,mergefinalfil:0,modul:0,msk:0,packag:0,pool:0,process:0,quick:0,requir:0,run:0,run_delli:0,run_iannot:0,run_iannotatesv:0,run_samblast:0,run_targetseqview:0,sampl:0,sortbambycoordin:0,sortbambyreadnam:0,structur:[0,1],submodul:0,tabl:1,take:0,transcript:0,usag:0,util:0}}) \ No newline at end of file diff --git a/docs/_build/json/_sources/iCallSV.txt b/docs/_build/json/_sources/iCallSV.txt index 210668a..8b8d8a8 100644 --- a/docs/_build/json/_sources/iCallSV.txt +++ b/docs/_build/json/_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 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    iCallSV: Structural Aberration Detection from NGS datasets\u00b6

    \n\n
    \n

    Required Packages\u00b6

    \n

    We require that you install:

    \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
    pandas:v0.16.2
    biopython:v1.65
    pysam:v0.8.4
    pyvcf:0.6.7
    Delly:v0.7.3
    targetSeqView:master
    iAnnotateSV:v1.0.5
    \n
    \n
    \n

    Required Data Files\u00b6

    \n

    This files are given in the data folder inside iCallSV.

    \n\n\n\n\n\n\n\n\n\n\n\n\n\n
    BlackListFile:

    (blacklist.txt) Tab-delimited file wihout header having black listed regions in order:

    \n
    \n

    chromosome 1, breakpoint 1, chromosome 2, breakpoint 2

    \n
    \n\n\n\n\n\n\n\n
    Example:7 140498077 5 175998094
    \n
    BlackListGenes:

    (blacklistgenes.txt) Gene listed one per line wihout header that are to be removed

    \n\n\n\n\n\n\n\n
    Example:

    LINC00486

    \n

    CNOT4

    \n
    \n
    HotspotFile:

    (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:

    \n
    \n

    chromosome, start, end, name

    \n
    \n\n\n\n\n\n\n\n
    Example:2 29416089 30143525 ALK
    \n
    GenesToKeep:

    (genesToInclude.txt) Gene listed one per line wihout header that are to be kept

    \n\n\n\n\n\n\n\n
    Example:

    ALK

    \n

    BRAF

    \n
    \n
    \n
    \n
    \n

    Configuration File Format\u00b6

    \n
    #~~~Template configuration file to run iCallSV~~~#\n#### Path to python executable ###\n[Python]\nPYTHON:\n#### Path to R executable and R Lib ###\n[R]\nRHOME:\nRLIB:\n#### Path to delly, bcftools executables and Version of delly (supports only 0.7.3)###\n[SVcaller]\nDELLY:\nDellyVersion:\nBCFTOOLS:\n#### Path to hg19 Referece Fasta file ###\n[ReferenceFasta]\nREFFASTA:\n#### Path to file containing regions to exclude please follow Delly documentation for this ###\n[ExcludeRegion]\nEXREGIONS:\n#### Path to file containing regions to where lenient threshold will be used; and file containing genes to keep ###\n[HotSpotRegions]\nHotspotFile:\nGenesToKeep:\n#### Path to file containing regions/genes to filter ###\n[BlackListRegions]\nBlackListFile:\nBlackListGenes:\n#### Path to samtools executable ###\n[SAMTOOLS]\nSAMTOOLS:\n#### Path to iAnnotateSV.py and all its required files, please follow iAnnotateSV documentation ###\n[iAnnotateSV]\nANNOSV:\nGENOMEBUILD:\nDISTANCE:\nCANONICALTRANSCRIPTFILE:\nUNIPROTFILE:\nCosmicCensus:\nRepeatRegionAnnotation:\nDGvAnnotations:\n#### TargetSeqView Parameters ###\n[TargetSeqView]\nCalculateConfidenceScore:\nGENOMEBUILD:\nReadLength:\n#### Parameters to run Delly ###\n[ParametersToRunDelly]\nMAPQ: 20\nNumberOfProcessors: 4\n[ParametersToFilterDellyResults]\n####Case Allele Fraction Hotspot####\nCaseAltFreqHotspot: 0.05\n####Total Case Coverage Hotspot#####\nCaseCoverageHotspot = 5\n####Control Allele Fraction Hotspot####\nControlAltFreqHotspot = 0\n####Case Allele Fraction####\nCaseAltFreq: 0.08\n####Total Case Coverage#####\nCaseCoverage = 8\n####Control Allele Fraction####\nControlAltFreq = 0\n###Overall Supporting Read-pairs ###\nOverallSupportingReads: 5\n###Overall Supporting Read-pairs Hotspot ###\nOverallSupportingReadsHotspot: 3\n###Overall Supporting splitreads ###\nOverallSupportingSplitReads: 0\n###Overall Supporting splitreads Hotspot ###\nOverallSupportingSplitReadsHotspot: 0\n###Case Supporting Read-pairs ###\nCaseSupportingReads: 2\n###Case Supporting splitreads ###\nCaseSupportingSplitReads: 0\n###Case Supporting Read-pairs Hotspot ###\nCaseSupportingReadsHotspot: 1\n###Case Supporting splitreads Hotspot ###\nCaseSupportingSplitReadsHotspot: 0\n###Control Supporting Read-pairs ###\nControlSupportingReads: 5\n###Control Supporting Read-pairs Hotspot ###\nControlSupportingReadsHotspot: 5\n###Control Supporting splitreads ###\nControlSupportingSplitReads: 5\n###Control Supporting splitreads Hotspot ###\nControlSupportingSplitReadsHotspot: 5\n###Length of Structural Variant###\nLengthOfSV: 500\n###Overall Mapping Quality Threshold###\nOverallMapq: 20\n###Overall Mapping Quality Threshold Hotspot###\nOverallMapqHotspot: 5\n
    \n
    \n
    \n
    \n

    Quick Usage\u00b6

    \n
    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\n
    \n
    \n
    > python iCallSV.py -h\n\nusage: iCallSV.py [-h] [-v] [-V] -sc config.ini -abam caseBAMFile.bam -bbam\n                  controlBAMFile.bam -aId caseID -bId controlID -o\n                  /somepath/output -op TumorID\n\niCallSV.iCallSV -- wrapper to run iCallSV package\n\n  Created by Ronak H Shah on 2015-03-30.\n  Copyright 2015-2016 Ronak H Shah. All rights reserved.\n\n  Licensed under the Apache License 2.0\n  http://www.apache.org/licenses/LICENSE-2.0\n\n  Distributed on an "AS IS" basis without warranties\n  or conditions of any kind, either express or implied.\n\nUSAGE\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -v, --verbose         set verbosity level [default: True]\n  -V, --version         show program's version number and exit\n  -sc config.ini, --svConfig config.ini\n                        Full path to the structural variant configuration\n  -abam caseBAMFile.bam, --caseBam caseBAMFile.bam\n                        Full path to the case bam file\n  -bbam controlBAMFile.bam, --controlBam controlBAMFile.bam\n                        Full path to the control bam file\n  -aId caseID, --caseId caseID\n                        Id of the case to be analyzed, this will be the sub-\n                        folder\n  -bId controlID, --controlId controlID\n                        Id of the control to be used, this will be used for\n                        filtering variants\n  -o /somepath/output, --outDir /somepath/output\n                        Full Path to the output dir.\n  -op TumorID, --outPrefix TumorID\n                        Id of the Tumor bam file which will be used as the\n                        prefix for output files\n
    \n
    \n
    \n
    \n

    Utilities\u00b6

    \n

    This is only for MSK-IMPACT internal samples

    \n
    > python iCallSV_dmp_wrapper.py -h\n\nusage: iCallSV_dmp_wrapper.py [options]\n\nRun iCallSV on selected pools using MSK data\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -fl folders.fof, --folderList folders.fof\n                        Full path folders file of files.\n  -qc /some/path/qcLocation, --qcLocation /some/path/qcLocation\n                        Full path qc files.\n  -b /some/path/bamlocation, --bamLocation /some/path/bamlocation\n                        Full path bam files.\n  -P /somepath/python, --python /somepath/python\n                        Full path Pyhton executables.\n  -icsv /somepath/iCallSV.py, --iCallSV /somepath/iCallSV.py\n                        Full path iCallSV.py executables.\n  -conf /somepath/template.ini, --iCallSVconf /somepath/template.ini\n                        Full path configuration file to run iCallSV\n  -q all.q or clin.q, --queue all.q or clin.q\n                        Name of the SGE queue\n  -qsub /somepath/qsub, --qsubPath /somepath/qsub\n                        Full Path to the qsub executables of SGE.\n  -t 5, --threads 5     Number of Threads to be used to run iCallSV\n  -v, --verbose         make lots of noise [default]\n  -o /somepath/output, --outDir /somepath/output\n                        Full Path to the output dir.\n
    \n
    \n
    \n
    \n

    Submodules\u00b6

    \n
    \n

    iCallSV.FilterDellyCalls module\u00b6

    \n
    \n

    FilterDellyCalls\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will filter calls made by Delly which are in a VCF format
    \n
    \n
    \niCallSV.FilterDellyCalls.GetCaseFlag(caseDR, caseDV, preciseFlag, caseRR, caseRV, caseAltFreq, caseTotalCount)[source]\u00b6
    \n

    This will check if the case sample passes or not

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • caseDR (int) – int representing number of reference reads for case reported by delly
      • \n
    • caseDV (int) – int representing number of variant reads for case reported by delly
      • \n
    • preciseFlag (str) – str representing if an event is precise or imprecise
      • \n
    • caseRR (int) – int representing number of split reference reads for case reported by delly
      • \n
    • caseRV (int) – int representing number of split variant reads for case reported by delly
      • \n
    • caseAltFreq (float) – float representing altratio threshold for case
      • \n
    • caseTotalCount (int) – int repeseting readcount threshold for case
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.FilterDellyCalls.GetControlFlag(controlDR, controlDV, preciseFlag, controlRR, controlRV, controlAltFreq)[source]\u00b6
    \n

    This will check if the control sample passes or not

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • controlDR (int) – int representing number of reference reads for control reported by delly
      • \n
    • controlDV (int) – int representing number of variant reads for control reported by delly
      • \n
    • preciseFlag (str) – str representing if an event is precise or imprecise
      • \n
    • controlRR (int) – int representing number of split reference reads for control reported by delly
      • \n
    • controlRV (int) – int representing number of split variant reads for control reported by delly
      • \n
    • controlAltFreq (float) – float representing altratio threshold for control
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.FilterDellyCalls.GetFilteredRecords(dellyVarialbles, thresholdVariables, hotspotDict, blacklist)[source]\u00b6
    \n

    This will Filter one record at a time

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • dellyVariables (str) – str having all delly variables separated by ”,”
      • \n
    • thresholdVariables (str) – str having all delly threshold variables separated by ”,”
      • \n
    • hotspotDict (dict) – A dict containing hotspot regions
      • \n
    • blacklist (list) – A list containing blacklist regions
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.FilterDellyCalls.run(inputVcf, outputDir, controlId, caseID, hotspotFile, blacklistFile, svlength, mapq, mapqHotspot, caseAltFreqHotspot, caseTotalCountHotspot, controlAltFreqHotspot, caseAltFreq, caseTotalCount, controlAltFreq, peSupport, srSupport, peSupportHotspot, srSupportHotspot, peSupportCase, srSupportCase, peSupportHotspotCase, srSupportHotspotCase, peSupportControl, srSupportControl, peSupportHotspotControl, srSupportHotspotControl, verbose)[source]\u00b6
    \n

    ``main:``Filter calls made by Delly which are in a VCF format

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • inputVcf (str) – Input VCF file name with path
      • \n
    • outputDir (str) – Output directory
      • \n
    • controlId (str) – Control Sample ID (Should be part of Sample Name in VCF)
      • \n
    • caseID (str) – Case Sample ID (Should be part of Sample Name in VCF)
      • \n
    • hospotFile (str) – List of Genes that have Hotspot Structural Variants (Tab-delimited Format without header:chr start end geneName).
      • \n
    • blacklistFile (str) – List of Genes that have blacklist of Structural Variants (Tab-delimited Format without header:chr start1 chr2 start2; where chr1==chr2, end==start2).
      • \n
    • caseAltFreq (float) – Alternate Allele Frequency threshold for case
      • \n
    • caseTotalCount (int) – Total ReadCount threshold for case
      • \n
    • ccontrolAltFreq (flaot) – Alternate Allele Frequency threshold for control
      • \n
    • peSupport (int) – overall pair-end read support threshold for the event
      • \n
    • srSupport (int) – overall split-reads support threshold for the event
      • \n
    • peSupportHotspot (int) – overall pair-end read support threshold for the event in hot-spot region
      • \n
    • srSupportHotspot (int) – overall split-reads support threshold for the event in hot-spot region
      • \n
    • peSupportCase (int) – pair-end read support threshold for the event in the Case sample
      • \n
    • srSupportCase (int) – split-reads support threshold for the event in the Case sample
      • \n
    • peSupportHotspotCase (int) – pair-end read support threshold for the event in hot-spot region for the Case sample
      • \n
    • srSupportHotspotCase (int) – split-reads support threshold for the event in hot-spot region for the Case sample
      • \n
    • peSupportControl (int) – pair-end read support threshold for the event in the Control sample
      • \n
    • srSupportControl (int) – split-reads support threshold for the event in the Control sample
      • \n
    • peSupportHotspotControl (int) – pair-end read support threshold for the event in hot-spot region for the Control sample
      • \n
    • srSupportHotspotControl (int) – split-reads support threshold for the event in hot-spot region for the Control sample
      • \n
    • svlength (int) – length of the structural variants
      • \n
    • mapq (int) – overall mapping quality
      • \n
    • mapqHotspot (int) – mapping quality for hot-spots
      • \n
    \n
    Returns:

    A str name of filtered vcf file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.Run_Delly module\u00b6

    \n
    \n

    Run_Delly\u00b6

    \n\n\n\n\n\n\n\n
    Description:Runs the delly program on case and control bam file to give its results
    \n
    \n
    \niCallSV.Run_Delly.run(delly, version, bcftools, analysisType, reference, controlBam, caseBam, caseId, mapq, excludeRegions, outputdir, verbose, debug)[source]\u00b6
    \n

    This will Runs the delly program on case and control bam file to give its\nresults.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • delly (str) – Path to delly executables (0.7.3 or above)
      • \n
    • bcftools (str) – Path to bcftools executables (1.3.1 or above)
      • \n
    • type (str) – What ot run in delly, DEL:Deletion, DUP: Duplication,TRA:Translocation, INV:Inversion
      • \n
    • reference (str) – Reference Genome that was used to align the reads.
      • \n
    • controlBam (str) – Path to control/normal bam file
      • \n
    • caseBam (str) – Path to case/tumor bam file
      • \n
    • controlID (str) – Id of the control/normal sample
      • \n
    • caseID (str) – Id of the case/tumor sample
      • \n
    • mapq (int) – mapping quality cutoff for delly
      • \n
    • excludeRegions (str) – Regions to be excluded for calling structural variation.
      • \n
    • outputdir (str) – directory for the output of delly
      • \n
    • debug (bool) – If you just wish to test what we will do
      • \n
    \n
    Returns:

    str of the output vcf

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.Run_iAnnotateSV module\u00b6

    \n
    \n

    Run_iAnnotate\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will run iAnnotateSV package
    \n
    \n
    \niCallSV.Run_iAnnotateSV.run(python, iAnnotateSV, build, distance, canonicalTranscriptFile, uniprotFile, cosmicFile, repeatregionFile, dgvFile, inputTabFile, outputPrefix, outputDir)[source]\u00b6
    \n

    This module will run iAnnotateSV package.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • python (str) – Location for the python executable.
      • \n
    • iAnnotateSV (str) – Location of the wrapper iAnnotateSV package (iAnnotateSV.py)
      • \n
    • build (str) – Which human reference file to be used, hg18,hg19 or hg38
      • \n
    • inputTabFile (str) – Tab-Delimited Input FIle compatible with iAnnotateSV package.
      • \n
    • outputPrefix (str) – Prefix of the output files/DIR with Annotations and images
      • \n
    • outputDir (str) – Name of the output directory where the outputPrefix will be written
      • \n
    • uniprotFile (str) – Location for ucsc uniprot file
      • \n
    • cosmicFile (str) – Location for cosmic census file
      • \n
    • repeatregionFile (str) – Location for repeat region file
      • \n
    • dgvFile (str) – Location for database of Genomic Variants file
      • \n
    \n
    Returns:

    str of the output file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.Run_samblaster module\u00b6

    \n
    \n

    Run_samblaster\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will run samblaster for extracting discordant and spit reads in sam format
    \n
    \n
    \niCallSV.Run_samblaster.run(samtools, samblaster, bamFile, discordantFileName, splitFileName, outputDir)[source]\u00b6
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.Run_targetSeqView module\u00b6

    \n
    \n

    Run_targetSeqView\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will run targetSeqView
    \n
    \n
    \niCallSV.Run_targetSeqView.run(RLocation, targetSeqView, nodes, bamFilePath, svFile, build, readLength, outputDir, outsvFileName)[source]\u00b6
    \n

    This module will run targetSeqView.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • RLocation (str) – Location of the R executable (>3.1.2).
      • \n
    • targetSeqView (str) – Location of R script that will run tragetSeqView
      • \n
    • nodes (int) – Number of parallel nodes for running targetSeqView
      • \n
    • bamFile (str) – Location of the bamFile which has the structural variant events.
      • \n
    • svFile (str) – targetSeqView compatible input structural variant file.
      • \n
    • build (str) – Which human reference file to be used, hg18,hg19 or hg38
      • \n
    • readLength (int) – Sequencing Read Length (101)
      • \n
    • outputDir (str) – Directory for output files
      • \n
    • outsvFile (str) – Name of the output structural variant file that has added confidence score to it.
      • \n
    \n
    Returns:

    str of the output file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.checkBlackList module\u00b6

    \n
    \n

    checkBlackList\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will read the Black List file and tell if and event is blacklisted or not
    \n
    \n
    \niCallSV.checkBlackList.CheckIfItIsBlacklisted(chr1, start1, chr2, start2, blacklist, extention)[source]\u00b6
    \n

    Check if coordinate are present in the blacklist region file

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • chr1 (str) – str of the breakpoint in first chromosome
      • \n
    • start1 (int) – int of the start location of the breakpoint in first chromosome
      • \n
    • chr2 (str) – str of the breakpoint in second chromosome
      • \n
    • start2 (int) – int of the start location of the breakpoint in second chromosome
      • \n
    • blacklist (list) – A list containing black listed regions
      • \n
    • extension (int) – an value for search in positive and negative direction of the start1 and start2 location
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.checkBlackList.ReadBlackListFile(BlackListFile)[source]\u00b6
    \n

    Read the blacklist region file

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:BlackListFile (str) – str of file to be read.
    Returns:A list containing black listed regions.
    Return type:list.
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.checkHotSpotList module\u00b6

    \n
    \n

    checkHotSpotList\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will read the hotspot file and tell if it is a hotspot or not
    \n
    \n
    \niCallSV.checkHotSpotList.CheckIfItIsHotspot(chr1, start1, chr2, start2, hotspotDict)[source]\u00b6
    \n

    Check if coordinate are present in the hotspot region file

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • chr1 (str) – str of the breakpoint in first chromosome
      • \n
    • start1 (int) – int of the start location of the breakpoint in first chromosome
      • \n
    • chr2 (str) – str of the breakpoint in second chromosome
      • \n
    • start2 (int) – int of the start location of the breakpoint in second chromosome
      • \n
    • hotspotDict (dict) – A dict containing hotspot regions
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.checkHotSpotList.ReadHotSpotFile(HotSpotFile)[source]\u00b6
    \n

    Read the HotSpot region file

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:HotSpotFile (str) – str of file to be read.
    Returns:A dict containing hotspot regions
    Return type:dict
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.checkparameters module\u00b6

    \n
    \n

    checkparameters\u00b6

    \n\n\n\n\n\n\n\n
    Description:This modules checks the parameters for various type of inputs.
    \n
    \n
    \niCallSV.checkparameters.checkDellyAnalysisType(varaibleToCheck)[source]\u00b6
    \n

    Check if the variable for Delly analysis exists or not`

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:variableToCheck (str) – check if str is DEL|DUP|INV|TRA
    Returns:None
    Return type:None
    \n
    \n\n
    \n
    \niCallSV.checkparameters.checkDir(folderToCheck)[source]\u00b6
    \n

    Check if the folder exists or not`

    \n

    str.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:folderToCheck (str) – Name of the folder to be checked.
    Returns:None
    Return type:None
    \n
    \n\n
    \n
    \niCallSV.checkparameters.checkEmpty(variableToCheck, variableName)[source]\u00b6
    \n

    Check if the variable is None or not`

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • variableToCheck (str) – check if str is None or not
      • \n
    • variableName (str) – Name of the None object to be verified
      • \n
    \n
    Returns:

    None

    \n
    Return type:

    None

    \n
    \n
    \n\n
    \n
    \niCallSV.checkparameters.checkFile(fileToCheck)[source]\u00b6
    \n

    Check if the file exists or not`

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:fileToCheck (str) – Name of the file to be checked.
    Returns:None
    Return type:None
    \n
    \n\n
    \n
    \niCallSV.checkparameters.checkInt(variableToCheck, variableName)[source]\u00b6
    \n

    Check if the variable is int or not`

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • variableToCheck (int) – Check if it is int or not
      • \n
    • variableName (str) – Name of the int object to be verified
      • \n
    \n
    Returns:

    None

    \n
    Return type:

    None

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.combineVCF module\u00b6

    \n
    \n

    combineVCF\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will combine multiple vcf file with same headers
    \n
    \n
    \niCallSV.combineVCF.run(vcfFiles, combinedVCF, verbose)[source]\u00b6
    \n

    This will combine multiple vcf file with same headers

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • vcfFiles (list) – a list of .vcf files to be combined
      • \n
    • combinedVCF (str) – str for the output of combined vcf files
      • \n
    • verbose (bool) – a boolean
      • \n
    \n
    Returns:

    A str name of combined vcf file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.dellyVcf2Tab module\u00b6

    \n
    \n

    dellyVcf2Tab\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module converts the Delly Vcf file having tumor normal, to tab-delimited format for input to iAnnotateSV
    \n
    \n
    \niCallSV.dellyVcf2Tab.vcf2tab(vcfFile, outputDir, verbose)[source]\u00b6
    \n

    This converts the Delly Vcf file having tumor normal, to tab-delimited format for input to iAnnotateSV

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • vcfFile (str) – str of vcf file to be converted
      • \n
    • outputDir (str) – str for the output directory
      • \n
    • verbose (bool) – a boolean
      • \n
    \n
    Returns:

    A str name of tab-delimited file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.dellyVcf2targetSeqView module\u00b6

    \n
    \n

    dellyVcf2targetSeqView\u00b6

    \n\n\n\n\n\n\n\n
    Description:Convert VCF to targetSeqView
    \n
    \n
    \niCallSV.dellyVcf2targetSeqView.Convert2targetSeqView(sampleName, sampleBamName, sampleSplitBamName, vcfFile, outputDir, outputFileName)[source]\u00b6
    \n

    This converts the Delly Vcf file having tumor normal, to tab-delimited format for input to targetSeqView

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • sampleName (str) – str for the name of the sample being analyzed
      • \n
    • sampleBamName (str) – str for the pair-end reads bam file
      • \n
    • sampleSplitBamName (str) – str for the split reads bam file
      • \n
    • vcfFile (str) – str of vcf file to be converted
      • \n
    • outputDir (str) – str for the output directory
      • \n
    • outputFileName (str) – str for the output File
      • \n
    \n
    Returns:

    A str name of tab-delimited file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.filterAnnotatedSV module\u00b6

    \n
    \n

    filterAnnotatedSV\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will filter calls from the merged file
    \n
    \n
    \niCallSV.filterAnnotatedSV.checkBlackListGene(gene1, gene2, blacklistGenes)[source]\u00b6
    \n

    This will check for blacklisted genes

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • gene1 (str) – str for the name of gene at breakpoint 1
      • \n
    • gene2 (str) – str for the name of gene at breakpoint 2
      • \n
    • blacklistGenes (list) – list containing blacklisted genes
      • \n
    • genesToKeepFile (str) – str for the txt file containing genes to keep
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.filterAnnotatedSV.checkEventInIntronFlag(gene1, gene2, site1, site2)[source]\u00b6
    \n

    This will Check if the event is in the intron only and not affecting\nsplicing

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • gene1 (str) – str for the name of gene at breakpoint 1
      • \n
    • gene2 (str) – str for the name of gene at breakpoint 2
      • \n
    • site1 (str) – str for the description of site in breakpoint 1
      • \n
    • site2 (str) – str for the description of site in breakpoint 2
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.filterAnnotatedSV.checkGeneListToKeep(gene1, gene2, keepGenes)[source]\u00b6
    \n
    \n\n
    \n
    \niCallSV.filterAnnotatedSV.run(inputTxt, outputDir, outPrefix, blacklistGenesFile, genesToKeepFile, verbose)[source]\u00b6
    \n

    This will filter sv calls from the final merged file.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • inputTxt (str) – str for the txt file to be filtered
      • \n
    • outputDir (str) – str for the output directory
      • \n
    • outputPrefix (str) – str prefix for the output File
      • \n
    • blacklistGenesFile (str) – str for the txt file containing blacklisted genes
      • \n
    • genesToKeepFile (str) – str for the txt file containing genes to keep
      • \n
    • verbose (bool) – a boolean
      • \n
    \n
    Returns:

    A str name of final sv file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.iCallSV module\u00b6

    \n
    \n

    iCallSV\u00b6

    \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
    Description:

    iCallSV is a wrapper to the iCallSV package which facilitates calling structural variants from Next Generation Sequencing methods such as Illumina

    \n
    author:

    Ronak H Shah

    \n
    copyright:
      \n
    1. 2015-2016 by Ronak H Shah for Memorial Sloan Kettering Cancer Center. All rights reserved.
      2. \n
    \n
    license:

    Apache License 2.0

    \n
    contact:

    rons.shah@gmail.com

    \n
    \n
    \n
    \n
    \n

    iCallSV.iCallSV_dmp_wrapper module\u00b6

    \n
    \n

    iCallSV_dmp_wrapper\u00b6

    \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
    Description:

    iCallSV is a wrapper to run the iCallSV package on MSKCC data

    \n
    author:

    Ronak H Shah

    \n
    copyright:
      \n
    1. 2015-2016 by Ronak H Shah for Memorial Sloan Kettering Cancer Center. All rights reserved.
      2. \n
    \n
    license:

    Apache License 2.0

    \n
    contact:

    rons.shah@gmail.com

    \n
    deffield updated:
     

    Updated

    \n
    \n
    \n
    \niCallSV.iCallSV_dmp_wrapper.RunJob(cmd)[source]\u00b6
    \n

    Given a command run the job.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:cmd (str) – str of command to be run on the local machine
    Returns:None
    Return type:None
    \n
    \n\n
    \n
    \niCallSV.iCallSV_dmp_wrapper.RunPerPool(titleFile, outdir, HSmetricsFileList, bamFileList, args)[source]\u00b6
    \n

    This will run the pool to be analyzed.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • titleFile (str) – str of meta information file
      • \n
    • outdir (str) – str of output directory
      • \n
    • HSmetricsFileList (list) – list of picard hsmetrics files
      • \n
    • bamFileList (list) – list of bam files
      • \n
    • args (Namespace) – Namespace of args to get other variables
      • \n
    \n
    Returns:

    None

    \n
    Return type:

    None

    \n
    \n
    \n\n
    \n
    \niCallSV.iCallSV_dmp_wrapper.SelectNormal(normal, poolnormal)[source]\u00b6
    \n

    Select the best possible normal.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • normal (str) – str of match normal
      • \n
    • poolnormal (str) – str of pool normal
      • \n
    \n
    Returns:

    str with decision whether to run matched or unmatched

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \niCallSV.iCallSV_dmp_wrapper.SetupRun(poolName, args)[source]\u00b6
    \n

    This will setup the run to be analyzed.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • poolName (str) – str of pool to be analyzed
      • \n
    • args (Namespace) – Namespace of args to get other variables
      • \n
    \n
    Returns:

    Multiple objects

    \n
    Return type:

    list

    \n
    \n
    \n\n
    \n
    \niCallSV.iCallSV_dmp_wrapper.getSubDirs(dirLocation)[source]\u00b6
    \n

    Get all sub directories.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:dirLocation (str) – str of directory location
    Returns:list of all sub directories
    Return type:list
    \n
    \n\n
    \n
    \niCallSV.iCallSV_dmp_wrapper.main()[source]\u00b6
    \n
    \n\n
    \n
    \niCallSV.iCallSV_dmp_wrapper.processor(i, jobqueue)[source]\u00b6
    \n

    Operate on a jobqueue.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • i (int) – count of the job
      • \n
    • jobqueue (Namespace) – Namespace for jobqueue
      • \n
    \n
    Returns:

    None

    \n
    Return type:

    None

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.launchThreads module\u00b6

    \n

    Created on December 21, 2015\nDescription: This module will be launching functions as threads\n@author: Ronak H Shah

    \n
    \n
    \nclass iCallSV.launchThreads.myThread(threadID, name, counter)[source]\u00b6
    \n

    Bases: threading.Thread

    \n
    \n
    \nrun()[source]\u00b6
    \n
    \n\n
    \n\n
    \n
    \niCallSV.launchThreads.print_time(threadName, delay, counter)[source]\u00b6
    \n
    \n\n
    \n
    \n

    iCallSV.launch_FilterDellyCalls module\u00b6

    \n
    \n

    launch_FilterDellyCalls\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will filter delly results and create filtered delly vcf files
    \n
    \n
    \niCallSV.launch_FilterDellyCalls.launch_filterdellycalls_for_different_analysis_type(args, config, sampleOutdirForDelly, del_vcf, dup_vcf, inv_vcf, tra_vcf)[source]\u00b6
    \n

    This will launch the filtering of delly calls in parallel.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • args (Namespace) – Namespace of args to get other variables
      • \n
    • config (Namespace) – configuration file passed to iCallSV
      • \n
    • sampleOutdirForDelly (str) – Output directory for delly vcf files.
      • \n
    • del_vcf (str) – Path to deletion based vcf file
      • \n
    • dup_vcf (str) – Path to duplication based vcf file
      • \n
    • inv_vcf (str) – Path to inversion based vcf file
      • \n
    • tra_vcf (str) – Path to translocation based vcf file
      • \n
    \n
    Returns:

    Multiple objects

    \n
    Return type:

    list

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.launch_Run_Delly module\u00b6

    \n
    \n

    launch_Run_Delly\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will be launching delly using Run_Delly
    \n
    \n
    \niCallSV.launch_Run_Delly.launch_delly_for_different_analysis_type(args, config, sampleOutdirForDelly)[source]\u00b6
    \n

    This will launch delly calls in parallel.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • args (Namespace) – Namespace of args to get other variables
      • \n
    • config (Namespace) – configuration file passed to iCallSV
      • \n
    • sampleOutdirForDelly (str) – Output directory for delly vcf files.
      • \n
    \n
    Returns:

    Multiple objects

    \n
    Return type:

    list

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.make_analysis_dir module\u00b6

    \n
    \n

    make_analysis_dir\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will make directory structure for running analysis
    \n
    \n
    \niCallSV.make_analysis_dir.makeOutputDir(args, tool)[source]\u00b6
    \n

    This will make the output directory tree.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:args (Namespace) – Namespace of args to get other variables
    Returns:Multiple objects
    Return type:list
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.makebamindex module\u00b6

    \n
    \n

    makebamindex\u00b6

    \n\n\n\n\n\n\n\n
    Description:Use PySAM to make bam index
    \n
    \n
    \niCallSV.makebamindex.MakeIndex(bamFile)[source]\u00b6
    \n

    This will make bam index if not there for a bam file using pysam.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:bamFile (str) – Path to bam file
    Returns:None
    Return type:None
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.mergeFinalFiles module\u00b6

    \n
    \n

    mergeFinalFiles\u00b6

    \n\n\n\n\n\n\n\n
    Description:Merge VCF, iAnnotateSV tab and targetSeqView tab file into a single tab-delimited file
    \n
    \n
    \niCallSV.mergeFinalFiles.run(aId, bId, vcfFile, annoTab, confTab, outDir, outputPrefix, verbose)[source]\u00b6
    \n

    This will Merge VCF, iAnnotateSV tab and targetSeqView tab file into a single tab-delimited file

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • aId (str) – Sample ID for case that has the structural abberations
      • \n
    • bId (str) – Sample ID for control
      • \n
    • vcfFile (str) – Delly filtered and merged VCF file
      • \n
    • annoTab (str) – iAnnotateSV tab-delimited file with annotations
      • \n
    • confTab (str) – targetSeqView tab-delimited file with probability score
      • \n
    • outputDir (str) – Directory to write the output file
      • \n
    • outputPrefix (str) – Output File Prefix
      • \n
    \n
    Returns:

    str of the tab-delimited file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.sortbamByCoordinate module\u00b6

    \n
    \n

    sortbamByCoordinate\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will sort bam file by coordinate
    \n
    \n
    \niCallSV.sortbamByCoordinate.sortBam(inputBam, outputBamName, outputDir)[source]\u00b6
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.sortbamByReadName module\u00b6

    \n
    \n

    sortbamByReadName\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will sort bam file by name
    \n
    \n
    \niCallSV.sortbamByReadName.sortBam(inputBam, outputBamName, outputDir)[source]\u00b6
    \n
    \n\n
    \n
    \n
    \n

    Module contents\u00b6

    \n
    \n
    \n", "alabaster_version": "0.7.7", "display_toc": true, "title": "iCallSV: Structural Aberration Detection from NGS datasets", "sourcename": "iCallSV.txt", "customsidebar": null, "current_page_name": "iCallSV", "next": null, "rellinks": [["genindex", "General Index", "I", "index"], ["py-modindex", "Python Module Index", "", "modules"], ["index", "iCallSV: Structural Aberration Detection from NGS datasets", "P", "previous"]], "meta": {}, "parents": [], "sidebars": null, "toc": "\n", "prev": {"link": "../", "title": "iCallSV: Structural Aberration Detection from NGS datasets"}, "metatags": ""} \ No newline at end of file +{"body": "
    \n

    iCallSV: Structural Aberration Detection from NGS datasets\u00b6

    \n
    \n
    \n

    Required Packages\u00b6

    \n

    We require that you install:

    \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
    pandas:v0.16.2
    biopython:v1.65
    pysam:v0.8.4
    pyvcf:0.6.7
    Delly:v0.7.3
    targetSeqView:master
    iAnnotateSV:v1.0.5
    \n
    \n
    \n

    Required Data Files\u00b6

    \n

    This files are given in the data folder inside iCallSV.

    \n\n\n\n\n\n\n\n\n\n\n\n\n\n
    BlackListFile:

    (blacklist.txt) Tab-delimited file wihout header having black listed regions in order:

    \n
    \n

    chromosome 1, breakpoint 1, chromosome 2, breakpoint 2

    \n
    \n\n\n\n\n\n\n\n
    Example:7 140498077 5 175998094
    \n
    BlackListGenes:

    (blacklistgenes.txt) Gene listed one per line wihout header that are to be removed

    \n\n\n\n\n\n\n\n
    Example:

    LINC00486

    \n

    CNOT4

    \n
    \n
    HotspotFile:

    (hotspotgenes.txt) Tab-delimited file wihout header having hotspot regions in order:

    \n
    \n

    chromosome, start, end, name

    \n
    \n\n\n\n\n\n\n\n
    Example:2 29416089 30143525 ALK
    \n
    GenesToKeep:

    (genesToInclude.txt) Gene listed one per line wihout header that are to be kept

    \n\n\n\n\n\n\n\n
    Example:

    ALK

    \n

    BRAF

    \n
    \n
    \n
    \n
    \n

    Configuration File Format\u00b6

    \n
    #~~~Template configuration file to run iCallSV~~~#\n#### Path to python executable ###\n[Python]\nPYTHON:\n#### Path to R executable and R Lib ###\n[R]\nRHOME:\nRLIB:\n#### Path to delly, bcftools executables and Version of delly (supports only 0.7.3)###\n[SVcaller]\nDELLY:\nDellyVersion:\nBCFTOOLS:\n#### Path to hg19 Referece Fasta file ###\n[ReferenceFasta]\nREFFASTA:\n#### Path to file containing regions to exclude please follow Delly documentation for this ###\n[ExcludeRegion]\nEXREGIONS:\n#### Path to file containing regions to where lenient threshold will be used; and file containing genes to keep ###\n[HotSpotRegions]\nHotspotFile:\nGenesToKeep:\n#### Path to file containing regions/genes to filter ###\n[BlackListRegions]\nBlackListFile:\nBlackListGenes:\n#### Path to samtools executable ###\n[SAMTOOLS]\nSAMTOOLS:\n#### Path to iAnnotateSV.py and all its required files, please follow iAnnotateSV documentation ###\n[iAnnotateSV]\nANNOSV:\nGENOMEBUILD:\nDISTANCE:\nCANONICALTRANSCRIPTFILE:\nUNIPROTFILE:\nCosmicCensus:\nRepeatRegionAnnotation:\nDGvAnnotations:\n#### TargetSeqView Parameters ###\n[TargetSeqView]\nCalculateConfidenceScore:\nGENOMEBUILD:\nReadLength:\n#### Parameters to run Delly ###\n[ParametersToRunDelly]\nMAPQ: 20\nNumberOfProcessors: 4\n[ParametersToFilterDellyResults]\n####Case Allele Fraction Hotspot####\nCaseAltFreqHotspot: 0.05\n####Total Case Coverage Hotspot#####\nCaseCoverageHotspot = 5\n####Control Allele Fraction Hotspot####\nControlAltFreqHotspot = 0\n####Case Allele Fraction####\nCaseAltFreq: 0.10\n####Total Case Coverage#####\nCaseCoverage = 10\n####Control Allele Fraction####\nControlAltFreq = 0\n###Overall Supporting Read-pairs ###\nOverallSupportingReads: 5\n###Overall Supporting Read-pairs Hotspot ###\nOverallSupportingReadsHotspot: 3\n###Overall Supporting splitreads ###\nOverallSupportingSplitReads: 0\n###Overall Supporting splitreads Hotspot ###\nOverallSupportingSplitReadsHotspot: 0\n###Case Supporting Read-pairs ###\nCaseSupportingReads: 2\n###Case Supporting splitreads ###\nCaseSupportingSplitReads: 0\n###Case Supporting Read-pairs Hotspot ###\nCaseSupportingReadsHotspot: 1\n###Case Supporting splitreads Hotspot ###\nCaseSupportingSplitReadsHotspot: 0\n###Control Supporting Read-pairs ###\nControlSupportingReads: 3\n###Control Supporting Read-pairs Hotspot ###\nControlSupportingReadsHotspot: 3\n###Control Supporting splitreads ###\nControlSupportingSplitReads: 3\n###Control Supporting splitreads Hotspot ###\nControlSupportingSplitReadsHotspot: 3\n###Length of Structural Variant###\nLengthOfSV: 500\n###Overall Mapping Quality Threshold###\nOverallMapq: 20\n###Overall Mapping Quality Threshold Hotspot###\nOverallMapqHotspot: 5\n
    \n
    \n
    \n
    \n

    Quick Usage\u00b6

    \n
    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\n
    \n
    \n
    python iCallSV.py -h\n\nusage: iCallSV.py [-h] [-v] [-V] -sc config.ini -abam caseBAMFile.bam -bbam\n                  controlBAMFile.bam -aId caseID -bId controlID -o\n                  /somepath/output -op TumorID\n\niCallSV.iCallSV -- wrapper to run iCallSV package\n\n  Created by Ronak H Shah on 2015-03-30.\n  Copyright 2015-2016 Ronak H Shah. All rights reserved.\n\n  Licensed under the Apache License 2.0\n  http://www.apache.org/licenses/LICENSE-2.0\n\n  Distributed on an "AS IS" basis without warranties\n  or conditions of any kind, either express or implied.\n\nUSAGE\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -v, --verbose         set verbosity level [default: True]\n  -V, --version         show program's version number and exit\n  -sc config.ini, --svConfig config.ini\n                        Full path to the structural variant configuration\n  -abam caseBAMFile.bam, --caseBam caseBAMFile.bam\n                        Full path to the case bam file\n  -bbam controlBAMFile.bam, --controlBam controlBAMFile.bam\n                        Full path to the control bam file\n  -aId caseID, --caseId caseID\n                        Id of the case to be analyzed, this will be the sub-\n                        folder\n  -bId controlID, --controlId controlID\n                        Id of the control to be used, this will be used for\n                        filtering variants\n  -o /somepath/output, --outDir /somepath/output\n                        Full Path to the output dir.\n  -op TumorID, --outPrefix TumorID\n                        Id of the Tumor bam file which will be used as the\n                        prefix for output files\n
    \n
    \n
    \n
    \n

    Utilities\u00b6

    \n
    \n

    Running iCallSV on MSK-IMPACT Pools\u00b6

    \n

    This is only for MSK-IMPACT internal samples

    \n
    python iCallSV_dmp_wrapper.py -h\n\nusage: iCallSV_dmp_wrapper.py [options]\n\nRun iCallSV on selected pools using MSK data\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -fl folders.fof, --folderList folders.fof\n                        Full path folders file of files.\n  -qc /some/path/qcLocation, --qcLocation /some/path/qcLocation\n                        Full path qc files.\n  -b /some/path/bamlocation, --bamLocation /some/path/bamlocation\n                        Full path bam files.\n  -P /somepath/python, --python /somepath/python\n                        Full path Pyhton executables.\n  -icsv /somepath/iCallSV.py, --iCallSV /somepath/iCallSV.py\n                        Full path iCallSV.py executables.\n  -conf /somepath/template.ini, --iCallSVconf /somepath/template.ini\n                        Full path configuration file to run iCallSV\n  -q all.q or clin.q, --queue all.q or clin.q\n                        Name of the SGE queue\n  -qsub /somepath/qsub, --qsubPath /somepath/qsub\n                        Full Path to the qsub executables of SGE.\n  -t 5, --threads 5     Number of Threads to be used to run iCallSV\n  -v, --verbose         make lots of noise [default]\n  -o /somepath/output, --outDir /somepath/output\n                        Full Path to the output dir.\n
    \n
    \n
    \n
    \n

    Taking the iCallSV and chechking for processed transcript/cDNA in samples\u00b6

    \n
    python check_cDNA_contamination.py -h\nusage: check_cDNA_contamination.py [options]\n\nCalculate cDNA contamination per sample based of the Structural Variants\nPipeline result\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -v, --verbose         make lots of noise [default]\n  -s SVfile.txt, --svFile SVfile.txt\n                        Location of the structural variant file to be used\n  -o cDNA_contamination, --outputFileName cDNA_contamination\n                        Full path name for the output file\n
    \n
    \n
    \n
    \n
    \n

    Submodules\u00b6

    \n
    \n

    iCallSV.iCallSV module\u00b6

    \n
    \n

    iCallSV\u00b6

    \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
    Description:

    iCallSV is a wrapper to the iCallSV package which facilitates calling structural variants from Next Generation Sequencing methods such as Illumina

    \n
    author:

    Ronak H Shah

    \n
    copyright:
      \n
    1. 2015-2016 by Ronak H Shah for Memorial Sloan Kettering Cancer Center. All rights reserved.
      2. \n
    \n
    license:

    Apache License 2.0

    \n
    contact:

    rons.shah@gmail.com

    \n
    \n
    \n
    \n
    \n

    iCallSV.FilterDellyCalls module\u00b6

    \n
    \n

    FilterDellyCalls\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will filter calls made by Delly which are in a VCF format
    \n
    \n
    \niCallSV.FilterDellyCalls.GetCaseFlag(caseDR, caseDV, preciseFlag, caseRR, caseRV, caseAltFreq, caseTotalCount)[source]\u00b6
    \n

    This will check if the case sample passes or not

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • caseDR (int) – int representing number of reference reads for case reported by delly
      • \n
    • caseDV (int) – int representing number of variant reads for case reported by delly
      • \n
    • preciseFlag (str) – str representing if an event is precise or imprecise
      • \n
    • caseRR (int) – int representing number of split reference reads for case reported by delly
      • \n
    • caseRV (int) – int representing number of split variant reads for case reported by delly
      • \n
    • caseAltFreq (float) – float representing altratio threshold for case
      • \n
    • caseTotalCount (int) – int repeseting readcount threshold for case
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.FilterDellyCalls.GetControlFlag(controlDR, controlDV, preciseFlag, controlRR, controlRV, controlAltFreq)[source]\u00b6
    \n

    This will check if the control sample passes or not

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • controlDR (int) – int representing number of reference reads for control reported by delly
      • \n
    • controlDV (int) – int representing number of variant reads for control reported by delly
      • \n
    • preciseFlag (str) – str representing if an event is precise or imprecise
      • \n
    • controlRR (int) – int representing number of split reference reads for control reported by delly
      • \n
    • controlRV (int) – int representing number of split variant reads for control reported by delly
      • \n
    • controlAltFreq (float) – float representing altratio threshold for control
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.FilterDellyCalls.GetFilteredRecords(dellyVarialbles, thresholdVariables, hotspotDict, blacklist)[source]\u00b6
    \n

    This will Filter one record at a time

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • dellyVariables (str) – str having all delly variables separated by ”,”
      • \n
    • thresholdVariables (str) – str having all delly threshold variables separated by ”,”
      • \n
    • hotspotDict (dict) – A dict containing hotspot regions
      • \n
    • blacklist (list) – A list containing blacklist regions
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.FilterDellyCalls.run(inputVcf, outputDir, controlId, caseID, hotspotFile, blacklistFile, svlength, mapq, mapqHotspot, caseAltFreqHotspot, caseTotalCountHotspot, controlAltFreqHotspot, caseAltFreq, caseTotalCount, controlAltFreq, peSupport, srSupport, peSupportHotspot, srSupportHotspot, peSupportCase, srSupportCase, peSupportHotspotCase, srSupportHotspotCase, peSupportControl, srSupportControl, peSupportHotspotControl, srSupportHotspotControl, verbose)[source]\u00b6
    \n

    ``main:``Filter calls made by Delly which are in a VCF format

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • inputVcf (str) – Input VCF file name with path
      • \n
    • outputDir (str) – Output directory
      • \n
    • controlId (str) – Control Sample ID (Should be part of Sample Name in VCF)
      • \n
    • caseID (str) – Case Sample ID (Should be part of Sample Name in VCF)
      • \n
    • hospotFile (str) – List of Genes that have Hotspot Structural Variants (Tab-delimited Format without header:chr start end geneName).
      • \n
    • blacklistFile (str) – List of Genes that have blacklist of Structural Variants (Tab-delimited Format without header:chr start1 chr2 start2; where chr1==chr2, end==start2).
      • \n
    • caseAltFreq (float) – Alternate Allele Frequency threshold for case
      • \n
    • caseTotalCount (int) – Total ReadCount threshold for case
      • \n
    • ccontrolAltFreq (flaot) – Alternate Allele Frequency threshold for control
      • \n
    • peSupport (int) – overall pair-end read support threshold for the event
      • \n
    • srSupport (int) – overall split-reads support threshold for the event
      • \n
    • peSupportHotspot (int) – overall pair-end read support threshold for the event in hot-spot region
      • \n
    • srSupportHotspot (int) – overall split-reads support threshold for the event in hot-spot region
      • \n
    • peSupportCase (int) – pair-end read support threshold for the event in the Case sample
      • \n
    • srSupportCase (int) – split-reads support threshold for the event in the Case sample
      • \n
    • peSupportHotspotCase (int) – pair-end read support threshold for the event in hot-spot region for the Case sample
      • \n
    • srSupportHotspotCase (int) – split-reads support threshold for the event in hot-spot region for the Case sample
      • \n
    • peSupportControl (int) – pair-end read support threshold for the event in the Control sample
      • \n
    • srSupportControl (int) – split-reads support threshold for the event in the Control sample
      • \n
    • peSupportHotspotControl (int) – pair-end read support threshold for the event in hot-spot region for the Control sample
      • \n
    • srSupportHotspotControl (int) – split-reads support threshold for the event in hot-spot region for the Control sample
      • \n
    • svlength (int) – length of the structural variants
      • \n
    • mapq (int) – overall mapping quality
      • \n
    • mapqHotspot (int) – mapping quality for hot-spots
      • \n
    \n
    Returns:

    A str name of filtered vcf file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.Run_Delly module\u00b6

    \n
    \n

    Run_Delly\u00b6

    \n\n\n\n\n\n\n\n
    Description:Runs the delly program on case and control bam file to give its results
    \n
    \n
    \niCallSV.Run_Delly.run(delly, version, bcftools, analysisType, reference, controlBam, caseBam, caseId, mapq, excludeRegions, outputdir, verbose, debug)[source]\u00b6
    \n

    This will Runs the delly program on case and control bam file to give its\nresults.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • delly (str) – Path to delly executables (0.7.3 or above)
      • \n
    • bcftools (str) – Path to bcftools executables (1.3.1 or above)
      • \n
    • type (str) – What ot run in delly, DEL:Deletion, DUP: Duplication,TRA:Translocation, INV:Inversion
      • \n
    • reference (str) – Reference Genome that was used to align the reads.
      • \n
    • controlBam (str) – Path to control/normal bam file
      • \n
    • caseBam (str) – Path to case/tumor bam file
      • \n
    • controlID (str) – Id of the control/normal sample
      • \n
    • caseID (str) – Id of the case/tumor sample
      • \n
    • mapq (int) – mapping quality cutoff for delly
      • \n
    • excludeRegions (str) – Regions to be excluded for calling structural variation.
      • \n
    • outputdir (str) – directory for the output of delly
      • \n
    • debug (bool) – If you just wish to test what we will do
      • \n
    \n
    Returns:

    str of the output vcf

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.Run_iAnnotateSV module\u00b6

    \n
    \n

    Run_iAnnotate\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will run iAnnotateSV package
    \n
    \n
    \niCallSV.Run_iAnnotateSV.run(python, iAnnotateSV, build, distance, canonicalTranscriptFile, uniprotFile, cosmicFile, repeatregionFile, dgvFile, inputTabFile, outputPrefix, outputDir)[source]\u00b6
    \n

    This module will run iAnnotateSV package.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • python (str) – Location for the python executable.
      • \n
    • iAnnotateSV (str) – Location of the wrapper iAnnotateSV package (iAnnotateSV.py)
      • \n
    • build (str) – Which human reference file to be used, hg18,hg19 or hg38
      • \n
    • inputTabFile (str) – Tab-Delimited Input FIle compatible with iAnnotateSV package.
      • \n
    • outputPrefix (str) – Prefix of the output files/DIR with Annotations and images
      • \n
    • outputDir (str) – Name of the output directory where the outputPrefix will be written
      • \n
    • uniprotFile (str) – Location for ucsc uniprot file
      • \n
    • cosmicFile (str) – Location for cosmic census file
      • \n
    • repeatregionFile (str) – Location for repeat region file
      • \n
    • dgvFile (str) – Location for database of Genomic Variants file
      • \n
    \n
    Returns:

    str of the output file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.Run_samblaster module\u00b6

    \n
    \n

    Run_samblaster\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will run samblaster for extracting discordant and spit reads in sam format
    \n
    \n
    \niCallSV.Run_samblaster.run(samtools, samblaster, bamFile, discordantFileName, splitFileName, outputDir)[source]\u00b6
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.Run_targetSeqView module\u00b6

    \n
    \n

    Run_targetSeqView\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will run targetSeqView
    \n
    \n
    \niCallSV.Run_targetSeqView.run(RLocation, targetSeqView, nodes, bamFilePath, svFile, build, readLength, outputDir, outsvFileName)[source]\u00b6
    \n

    This module will run targetSeqView.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • RLocation (str) – Location of the R executable (>3.1.2).
      • \n
    • targetSeqView (str) – Location of R script that will run tragetSeqView
      • \n
    • nodes (int) – Number of parallel nodes for running targetSeqView
      • \n
    • bamFile (str) – Location of the bamFile which has the structural variant events.
      • \n
    • svFile (str) – targetSeqView compatible input structural variant file.
      • \n
    • build (str) – Which human reference file to be used, hg18,hg19 or hg38
      • \n
    • readLength (int) – Sequencing Read Length (101)
      • \n
    • outputDir (str) – Directory for output files
      • \n
    • outsvFile (str) – Name of the output structural variant file that has added confidence score to it.
      • \n
    \n
    Returns:

    str of the output file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.checkBlackList module\u00b6

    \n
    \n

    checkBlackList\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will read the Black List file and tell if and event is blacklisted or not
    \n
    \n
    \niCallSV.checkBlackList.CheckIfItIsBlacklisted(chr1, start1, chr2, start2, blacklist, extention)[source]\u00b6
    \n

    Check if coordinate are present in the blacklist region file

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • chr1 (str) – str of the breakpoint in first chromosome
      • \n
    • start1 (int) – int of the start location of the breakpoint in first chromosome
      • \n
    • chr2 (str) – str of the breakpoint in second chromosome
      • \n
    • start2 (int) – int of the start location of the breakpoint in second chromosome
      • \n
    • blacklist (list) – A list containing black listed regions
      • \n
    • extension (int) – an value for search in positive and negative direction of the start1 and start2 location
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.checkBlackList.ReadBlackListFile(BlackListFile)[source]\u00b6
    \n

    Read the blacklist region file

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:BlackListFile (str) – str of file to be read.
    Returns:A list containing black listed regions.
    Return type:list.
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.checkHotSpotList module\u00b6

    \n
    \n

    checkHotSpotList\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will read the hotspot file and tell if it is a hotspot or not
    \n
    \n
    \niCallSV.checkHotSpotList.CheckIfItIsHotspot(chr1, start1, chr2, start2, hotspotDict)[source]\u00b6
    \n

    Check if coordinate are present in the hotspot region file

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • chr1 (str) – str of the breakpoint in first chromosome
      • \n
    • start1 (int) – int of the start location of the breakpoint in first chromosome
      • \n
    • chr2 (str) – str of the breakpoint in second chromosome
      • \n
    • start2 (int) – int of the start location of the breakpoint in second chromosome
      • \n
    • hotspotDict (dict) – A dict containing hotspot regions
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.checkHotSpotList.ReadHotSpotFile(HotSpotFile)[source]\u00b6
    \n

    Read the HotSpot region file

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:HotSpotFile (str) – str of file to be read.
    Returns:A dict containing hotspot regions
    Return type:dict
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.checkparameters module\u00b6

    \n
    \n

    checkparameters\u00b6

    \n\n\n\n\n\n\n\n
    Description:This modules checks the parameters for various type of inputs.
    \n
    \n
    \niCallSV.checkparameters.checkDellyAnalysisType(varaibleToCheck)[source]\u00b6
    \n

    Check if the variable for Delly analysis exists or not`

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:variableToCheck (str) – check if str is DEL|DUP|INV|TRA
    Returns:None
    Return type:None
    \n
    \n\n
    \n
    \niCallSV.checkparameters.checkDir(folderToCheck)[source]\u00b6
    \n

    Check if the folder exists or not`

    \n

    str.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:folderToCheck (str) – Name of the folder to be checked.
    Returns:None
    Return type:None
    \n
    \n\n
    \n
    \niCallSV.checkparameters.checkEmpty(variableToCheck, variableName)[source]\u00b6
    \n

    Check if the variable is None or not`

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • variableToCheck (str) – check if str is None or not
      • \n
    • variableName (str) – Name of the None object to be verified
      • \n
    \n
    Returns:

    None

    \n
    Return type:

    None

    \n
    \n
    \n\n
    \n
    \niCallSV.checkparameters.checkFile(fileToCheck)[source]\u00b6
    \n

    Check if the file exists or not`

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:fileToCheck (str) – Name of the file to be checked.
    Returns:None
    Return type:None
    \n
    \n\n
    \n
    \niCallSV.checkparameters.checkInt(variableToCheck, variableName)[source]\u00b6
    \n

    Check if the variable is int or not`

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • variableToCheck (int) – Check if it is int or not
      • \n
    • variableName (str) – Name of the int object to be verified
      • \n
    \n
    Returns:

    None

    \n
    Return type:

    None

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.combineVCF module\u00b6

    \n
    \n

    combineVCF\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will combine multiple vcf file with same headers
    \n
    \n
    \niCallSV.combineVCF.run(vcfFiles, combinedVCF, verbose)[source]\u00b6
    \n

    This will combine multiple vcf file with same headers

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • vcfFiles (list) – a list of .vcf files to be combined
      • \n
    • combinedVCF (str) – str for the output of combined vcf files
      • \n
    • verbose (bool) – a boolean
      • \n
    \n
    Returns:

    A str name of combined vcf file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.dellyVcf2Tab module\u00b6

    \n
    \n

    dellyVcf2Tab\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module converts the Delly Vcf file having tumor normal, to tab-delimited format for input to iAnnotateSV
    \n
    \n
    \niCallSV.dellyVcf2Tab.vcf2tab(vcfFile, outputDir, verbose)[source]\u00b6
    \n

    This converts the Delly Vcf file having tumor normal, to tab-delimited format for input to iAnnotateSV

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • vcfFile (str) – str of vcf file to be converted
      • \n
    • outputDir (str) – str for the output directory
      • \n
    • verbose (bool) – a boolean
      • \n
    \n
    Returns:

    A str name of tab-delimited file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.dellyVcf2targetSeqView module\u00b6

    \n
    \n

    dellyVcf2targetSeqView\u00b6

    \n\n\n\n\n\n\n\n
    Description:Convert VCF to targetSeqView
    \n
    \n
    \niCallSV.dellyVcf2targetSeqView.Convert2targetSeqView(sampleName, sampleBamName, sampleSplitBamName, vcfFile, outputDir, outputFileName)[source]\u00b6
    \n

    This converts the Delly Vcf file having tumor normal, to tab-delimited format for input to targetSeqView

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • sampleName (str) – str for the name of the sample being analyzed
      • \n
    • sampleBamName (str) – str for the pair-end reads bam file
      • \n
    • sampleSplitBamName (str) – str for the split reads bam file
      • \n
    • vcfFile (str) – str of vcf file to be converted
      • \n
    • outputDir (str) – str for the output directory
      • \n
    • outputFileName (str) – str for the output File
      • \n
    \n
    Returns:

    A str name of tab-delimited file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.filterAnnotatedSV module\u00b6

    \n
    \n

    filterAnnotatedSV\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will filter calls from the merged file
    \n
    \n
    \niCallSV.filterAnnotatedSV.checkBlackListGene(gene1, gene2, blacklistGenes)[source]\u00b6
    \n

    This will check for blacklisted genes

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • gene1 (str) – str for the name of gene at breakpoint 1
      • \n
    • gene2 (str) – str for the name of gene at breakpoint 2
      • \n
    • blacklistGenes (list) – list containing blacklisted genes
      • \n
    • genesToKeepFile (str) – str for the txt file containing genes to keep
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.filterAnnotatedSV.checkEventInIntronFlag(gene1, gene2, site1, site2)[source]\u00b6
    \n

    This will Check if the event is in the intron only and not affecting\nsplicing

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • gene1 (str) – str for the name of gene at breakpoint 1
      • \n
    • gene2 (str) – str for the name of gene at breakpoint 2
      • \n
    • site1 (str) – str for the description of site in breakpoint 1
      • \n
    • site2 (str) – str for the description of site in breakpoint 2
      • \n
    \n
    Returns:

    A boolean tag indicating True or False

    \n
    Return type:

    bool

    \n
    \n
    \n\n
    \n
    \niCallSV.filterAnnotatedSV.checkGeneListToKeep(gene1, gene2, keepGenes)[source]\u00b6
    \n
    \n\n
    \n
    \niCallSV.filterAnnotatedSV.run(inputTxt, outputDir, outPrefix, blacklistGenesFile, genesToKeepFile, verbose)[source]\u00b6
    \n

    This will filter sv calls from the final merged file.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • inputTxt (str) – str for the txt file to be filtered
      • \n
    • outputDir (str) – str for the output directory
      • \n
    • outputPrefix (str) – str prefix for the output File
      • \n
    • blacklistGenesFile (str) – str for the txt file containing blacklisted genes
      • \n
    • genesToKeepFile (str) – str for the txt file containing genes to keep
      • \n
    • verbose (bool) – a boolean
      • \n
    \n
    Returns:

    A str name of final sv file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.utilities.iCallSV_dmp_wrapper module\u00b6

    \n
    \n
    \n

    iCallSV.utilities.check_cDNA_contamination module\u00b6

    \n
    \n
    \n

    iCallSV.launchThreads module\u00b6

    \n

    Created on December 21, 2015\nDescription: This module will be launching functions as threads\n@author: Ronak H Shah

    \n
    \n
    \nclass iCallSV.launchThreads.myThread(threadID, name, counter)[source]\u00b6
    \n

    Bases: threading.Thread

    \n
    \n
    \nrun()[source]\u00b6
    \n
    \n\n
    \n\n
    \n
    \niCallSV.launchThreads.print_time(threadName, delay, counter)[source]\u00b6
    \n
    \n\n
    \n
    \n

    iCallSV.launch_FilterDellyCalls module\u00b6

    \n
    \n

    launch_FilterDellyCalls\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will filter delly results and create filtered delly vcf files
    \n
    \n
    \niCallSV.launch_FilterDellyCalls.launch_filterdellycalls_for_different_analysis_type(args, config, sampleOutdirForDelly, del_vcf, dup_vcf, inv_vcf, tra_vcf)[source]\u00b6
    \n

    This will launch the filtering of delly calls in parallel.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • args (Namespace) – Namespace of args to get other variables
      • \n
    • config (Namespace) – configuration file passed to iCallSV
      • \n
    • sampleOutdirForDelly (str) – Output directory for delly vcf files.
      • \n
    • del_vcf (str) – Path to deletion based vcf file
      • \n
    • dup_vcf (str) – Path to duplication based vcf file
      • \n
    • inv_vcf (str) – Path to inversion based vcf file
      • \n
    • tra_vcf (str) – Path to translocation based vcf file
      • \n
    \n
    Returns:

    Multiple objects

    \n
    Return type:

    list

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.launch_Run_Delly module\u00b6

    \n
    \n

    launch_Run_Delly\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will be launching delly using Run_Delly
    \n
    \n
    \niCallSV.launch_Run_Delly.launch_delly_for_different_analysis_type(args, config, sampleOutdirForDelly)[source]\u00b6
    \n

    This will launch delly calls in parallel.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • args (Namespace) – Namespace of args to get other variables
      • \n
    • config (Namespace) – configuration file passed to iCallSV
      • \n
    • sampleOutdirForDelly (str) – Output directory for delly vcf files.
      • \n
    \n
    Returns:

    Multiple objects

    \n
    Return type:

    list

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.make_analysis_dir module\u00b6

    \n
    \n

    make_analysis_dir\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will make directory structure for running analysis
    \n
    \n
    \niCallSV.make_analysis_dir.makeOutputDir(args, tool)[source]\u00b6
    \n

    This will make the output directory tree.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:args (Namespace) – Namespace of args to get other variables
    Returns:Multiple objects
    Return type:list
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.makebamindex module\u00b6

    \n
    \n

    makebamindex\u00b6

    \n\n\n\n\n\n\n\n
    Description:Use PySAM to make bam index
    \n
    \n
    \niCallSV.makebamindex.MakeIndex(bamFile)[source]\u00b6
    \n

    This will make bam index if not there for a bam file using pysam.

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:bamFile (str) – Path to bam file
    Returns:None
    Return type:None
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.mergeFinalFiles module\u00b6

    \n
    \n

    mergeFinalFiles\u00b6

    \n\n\n\n\n\n\n\n
    Description:Merge VCF, iAnnotateSV tab and targetSeqView tab file into a single tab-delimited file
    \n
    \n
    \niCallSV.mergeFinalFiles.run(aId, bId, vcfFile, annoTab, confTab, outDir, outputPrefix, verbose)[source]\u00b6
    \n

    This will Merge VCF, iAnnotateSV tab and targetSeqView tab file into a single tab-delimited file

    \n\n\n\n\n\n\n\n\n\n\n\n
    Parameters:
      \n
    • aId (str) – Sample ID for case that has the structural abberations
      • \n
    • bId (str) – Sample ID for control
      • \n
    • vcfFile (str) – Delly filtered and merged VCF file
      • \n
    • annoTab (str) – iAnnotateSV tab-delimited file with annotations
      • \n
    • confTab (str) – targetSeqView tab-delimited file with probability score
      • \n
    • outputDir (str) – Directory to write the output file
      • \n
    • outputPrefix (str) – Output File Prefix
      • \n
    \n
    Returns:

    str of the tab-delimited file

    \n
    Return type:

    str

    \n
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.sortbamByCoordinate module\u00b6

    \n
    \n

    sortbamByCoordinate\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will sort bam file by coordinate
    \n
    \n
    \niCallSV.sortbamByCoordinate.sortBam(inputBam, outputBamName, outputDir)[source]\u00b6
    \n
    \n\n
    \n
    \n
    \n

    iCallSV.sortbamByReadName module\u00b6

    \n
    \n

    sortbamByReadName\u00b6

    \n\n\n\n\n\n\n\n
    Description:This module will sort bam file by name
    \n
    \n
    \niCallSV.sortbamByReadName.sortBam(inputBam, outputBamName, outputDir)[source]\u00b6
    \n
    \n\n
    \n
    \n
    \n

    Module contents\u00b6

    \n
    \n
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    \n

    iCallSV: Structural Aberration Detection from NGS datasets\u00b6

    \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
    Author:Ronak H Shah
    Contact:rons.shah@gmail.com
    Source code:http://github.com/rhshah/iCallSV
    Wiki:http://icallsv.readthedocs.io/en/latest/
    License:Apache License 2.0
    \n\"Code\n\n

    iCallSV is a Python library and command-line software toolkit to call structural aberrations from Next Generation DNA sequencing data. Behind the scenes it uses Delly2 to do structural variant calling. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and\nshort-read sequencing platforms such as Illumina.

    \n
    \n
    \n

    Citation\u00b6

    \n

    We are in the process of publishing a manuscript describing iCallSV as part of the Structural Variant Detection framework.\nIf you use this software in a publication, for now, please cite our website iCallSV.

    \n

    Contents:

    \n
    \n\n
    \n
    \n
    \n

    Indices and tables\u00b6

    \n\n
    \n", "alabaster_version": "0.7.7", "display_toc": true, "title": "iCallSV: Structural Aberration Detection from NGS datasets", "sourcename": "index.txt", "customsidebar": null, "current_page_name": "index", "next": {"link": "iCallSV/", "title": "iCallSV: Structural Aberration Detection from NGS datasets"}, "rellinks": [["genindex", "General Index", "I", "index"], ["py-modindex", "Python Module Index", "", "modules"], ["iCallSV", "iCallSV: Structural Aberration Detection from NGS datasets", "N", "next"]], "meta": {}, "parents": [], "sidebars": null, "toc": "\n", "prev": null, "metatags": ""} \ No newline at end of file +{"body": "
    \n

    iCallSV: Structural Aberration Detection from NGS datasets\u00b6

    \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
    Author:Ronak H Shah
    Contact:rons.shah@gmail.com
    Source code:http://github.com/rhshah/iCallSV
    Wiki:http://icallsv.readthedocs.io/en/latest/
    License:Apache License 2.0
    \n\"Code\n\n

    iCallSV is a Python library and command-line software toolkit to call structural aberrations from Next Generation DNA sequencing data. Behind the scenes it uses Delly2 to do structural variant calling. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and\nshort-read sequencing platforms such as Illumina.

    \n
    \n
    \n

    Citation\u00b6

    \n

    We are in the process of publishing a manuscript describing iCallSV as part of the Structural Variant Detection framework.\nIf you use this software in a publication, for now, please cite our website iCallSV.

    \n

    Contents:

    \n
    \n\n
    \n
    \n
    \n

    Indices and tables\u00b6

    \n\n
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"iCallSV.Run_iAnnotateSV": {"run": [0, 1, 1, ""]}, "iCallSV.sortbamByCoordinate": {"sortBam": [0, 1, 1, ""]}}, "titleterms": {"filterannotatedsv": 0, "icallsv_dmp_wrapp": 0, "launchthread": 0, "citat": 1, "process": 0, "sortbambyreadnam": 0, "modul": 0, "submodul": 0, "indic": 1, "dataset": [0, 1], "packag": 0, "sampl": 0, "file": 0, "tabl": 1, "dellyvcf2targetseqview": 0, "run_iannot": 0, "checkparamet": 0, "impact": 0, "detect": [0, 1], "from": [0, 1], "transcript": 0, "configur": 0, "run_targetseqview": 0, "filterdellycal": 0, "data": 0, "content": 0, "launch_run_delli": 0, "take": 0, "run_samblast": 0, "checkhotspotlist": 0, "cdna": 0, "run_delli": 0, "run": 0, "format": 0, "sortbambycoordin": 0, "usag": 0, "checkblacklist": 0, "util": 0, "launch_filterdellycal": 0, "icallsv": [0, 1], "make_analysis_dir": 0, "mergefinalfil": 0, "pool": 0, "check_cdna_contamin": 0, "combinevcf": 0, "msk": 0, "requir": 0, "structur": [0, 1], "dellyvcf2tab": 0, "aberr": [0, 1], "quick": 0, "run_iannotatesv": 0, "chechk": 0, "makebamindex": 0}} \ No newline at end of file diff --git a/docs/_build/latex/iCallSV.tex b/docs/_build/latex/iCallSV.tex index 6cc2e6c..4ea4884 100644 --- a/docs/_build/latex/iCallSV.tex +++ b/docs/_build/latex/iCallSV.tex @@ -21,7 +21,7 @@ \title{iCallSV Documentation} -\date{June 06, 2016} +\date{June 07, 2016} \release{} \author{Author} \newcommand{\sphinxlogo}{} @@ -248,38 +248,38 @@ \section{Required Data Files} \section{Configuration File Format} \label{iCallSV:configuration-file-format} \begin{Verbatim}[commandchars=\\\{\}] -\PYGZsh{}\PYGZti{}\PYGZti{}\PYGZti{}Template configuration file to run iCallSV\PYGZti{}\PYGZti{}\PYGZti{}\PYGZsh{} -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to python executable \PYGZsh{}\PYGZsh{}\PYGZsh{} -[Python] +\PYG{c+c1}{\PYGZsh{}\PYGZti{}\PYGZti{}\PYGZti{}Template configuration file to run iCallSV\PYGZti{}\PYGZti{}\PYGZti{}\PYGZsh{}} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to python executable \PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}Python\PYG{o}{]} PYTHON: -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to R executable and R Lib \PYGZsh{}\PYGZsh{}\PYGZsh{} -[R] +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to R executable and R Lib \PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}R\PYG{o}{]} RHOME: RLIB: -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to delly, bcftools executables and Version of delly (supports only 0.7.3)\PYGZsh{}\PYGZsh{}\PYGZsh{} -[SVcaller] +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to delly, bcftools executables and Version of delly (supports only 0.7.3)\PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}SVcaller\PYG{o}{]} DELLY: DellyVersion: BCFTOOLS: -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to hg19 Referece Fasta file \PYGZsh{}\PYGZsh{}\PYGZsh{} -[ReferenceFasta] +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to hg19 Referece Fasta file \PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}ReferenceFasta\PYG{o}{]} REFFASTA: -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to file containing regions to exclude please follow Delly documentation for this \PYGZsh{}\PYGZsh{}\PYGZsh{} -[ExcludeRegion] +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to file containing regions to exclude please follow Delly documentation for this \PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}ExcludeRegion\PYG{o}{]} EXREGIONS: -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to file containing regions to where lenient threshold will be used; and file containing genes to keep \PYGZsh{}\PYGZsh{}\PYGZsh{} -[HotSpotRegions] +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to file containing regions to where lenient threshold will be used; and file containing genes to keep \PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}HotSpotRegions\PYG{o}{]} HotspotFile: GenesToKeep: -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to file containing regions/genes to filter \PYGZsh{}\PYGZsh{}\PYGZsh{} -[BlackListRegions] +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to file containing regions/genes to filter \PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}BlackListRegions\PYG{o}{]} BlackListFile: BlackListGenes: -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to samtools executable \PYGZsh{}\PYGZsh{}\PYGZsh{} -[SAMTOOLS] +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to samtools executable \PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}SAMTOOLS\PYG{o}{]} SAMTOOLS: -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to iAnnotateSV.py and all its required files, please follow iAnnotateSV documentation \PYGZsh{}\PYGZsh{}\PYGZsh{} -[iAnnotateSV] +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Path to iAnnotateSV.py and all its required files, please follow iAnnotateSV documentation \PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}iAnnotateSV\PYG{o}{]} ANNOSV: GENOMEBUILD: DISTANCE: @@ -288,57 +288,57 @@ \section{Configuration File Format} CosmicCensus: RepeatRegionAnnotation: DGvAnnotations: -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} TargetSeqView Parameters \PYGZsh{}\PYGZsh{}\PYGZsh{} -[TargetSeqView] +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} TargetSeqView Parameters \PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}TargetSeqView\PYG{o}{]} CalculateConfidenceScore: GENOMEBUILD: ReadLength: -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Parameters to run Delly \PYGZsh{}\PYGZsh{}\PYGZsh{} -[ParametersToRunDelly] +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} Parameters to run Delly \PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{o}{[}ParametersToRunDelly\PYG{o}{]} MAPQ: 20 NumberOfProcessors: 4 -[ParametersToFilterDellyResults] -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Allele Fraction Hotspot\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{o}{[}ParametersToFilterDellyResults\PYG{o}{]} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Allele Fraction Hotspot\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}} CaseAltFreqHotspot: 0.05 -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Total Case Coverage Hotspot\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} -CaseCoverageHotspot = 5 -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Allele Fraction Hotspot\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} -ControlAltFreqHotspot = 0 -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Allele Fraction\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} -CaseAltFreq: 0.08 -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Total Case Coverage\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} -CaseCoverage = 8 -\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Allele Fraction\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{} -ControlAltFreq = 0 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Supporting Read\PYGZhy{}pairs \PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Total Case Coverage Hotspot\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{n+nv}{CaseCoverageHotspot} \PYG{o}{=} 5 +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Allele Fraction Hotspot\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{n+nv}{ControlAltFreqHotspot} \PYG{o}{=} 0 +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Allele Fraction\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}} +CaseAltFreq: 0.10 +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Total Case Coverage\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{n+nv}{CaseCoverage} \PYG{o}{=} 10 +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Allele Fraction\PYGZsh{}\PYGZsh{}\PYGZsh{}\PYGZsh{}} +\PYG{n+nv}{ControlAltFreq} \PYG{o}{=} 0 +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Supporting Read\PYGZhy{}pairs \PYGZsh{}\PYGZsh{}\PYGZsh{}} OverallSupportingReads: 5 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Supporting Read\PYGZhy{}pairs Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Supporting Read\PYGZhy{}pairs Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{}} OverallSupportingReadsHotspot: 3 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Supporting splitreads \PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Supporting splitreads \PYGZsh{}\PYGZsh{}\PYGZsh{}} OverallSupportingSplitReads: 0 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Supporting splitreads Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Supporting splitreads Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{}} OverallSupportingSplitReadsHotspot: 0 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Supporting Read\PYGZhy{}pairs \PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Supporting Read\PYGZhy{}pairs \PYGZsh{}\PYGZsh{}\PYGZsh{}} CaseSupportingReads: 2 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Supporting splitreads \PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Supporting splitreads \PYGZsh{}\PYGZsh{}\PYGZsh{}} CaseSupportingSplitReads: 0 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Supporting Read\PYGZhy{}pairs Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Supporting Read\PYGZhy{}pairs Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{}} CaseSupportingReadsHotspot: 1 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Supporting splitreads Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Case Supporting splitreads Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{}} CaseSupportingSplitReadsHotspot: 0 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Supporting Read\PYGZhy{}pairs \PYGZsh{}\PYGZsh{}\PYGZsh{} -ControlSupportingReads: 5 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Supporting Read\PYGZhy{}pairs Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{} -ControlSupportingReadsHotspot: 5 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Supporting splitreads \PYGZsh{}\PYGZsh{}\PYGZsh{} -ControlSupportingSplitReads: 5 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Supporting splitreads Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{} -ControlSupportingSplitReadsHotspot: 5 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Length of Structural Variant\PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Supporting Read\PYGZhy{}pairs \PYGZsh{}\PYGZsh{}\PYGZsh{}} +ControlSupportingReads: 3 +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Supporting Read\PYGZhy{}pairs Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{}} +ControlSupportingReadsHotspot: 3 +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Supporting splitreads \PYGZsh{}\PYGZsh{}\PYGZsh{}} +ControlSupportingSplitReads: 3 +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Control Supporting splitreads Hotspot \PYGZsh{}\PYGZsh{}\PYGZsh{}} +ControlSupportingSplitReadsHotspot: 3 +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Length of Structural Variant\PYGZsh{}\PYGZsh{}\PYGZsh{}} LengthOfSV: 500 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Mapping Quality Threshold\PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Mapping Quality Threshold\PYGZsh{}\PYGZsh{}\PYGZsh{}} OverallMapq: 20 -\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Mapping Quality Threshold Hotspot\PYGZsh{}\PYGZsh{}\PYGZsh{} +\PYG{c+c1}{\PYGZsh{}\PYGZsh{}\PYGZsh{}Overall Mapping Quality Threshold Hotspot\PYGZsh{}\PYGZsh{}\PYGZsh{}} OverallMapqHotspot: 5 \end{Verbatim} @@ -350,7 +350,7 @@ \section{Quick Usage} \end{Verbatim} \begin{Verbatim}[commandchars=\\\{\}] -\PYGZgt{} python iCallSV.py \PYGZhy{}h +python iCallSV.py \PYGZhy{}h usage: iCallSV.py [\PYGZhy{}h] [\PYGZhy{}v] [\PYGZhy{}V] \PYGZhy{}sc config.ini \PYGZhy{}abam caseBAMFile.bam \PYGZhy{}bbam controlBAMFile.bam \PYGZhy{}aId caseID \PYGZhy{}bId controlID \PYGZhy{}o @@ -395,10 +395,13 @@ \section{Quick Usage} \section{Utilities} \label{iCallSV:utilities} + +\subsection{Running iCallSV on MSK-IMPACT Pools} +\label{iCallSV:running-icallsv-on-msk-impact-pools} \textbf{This is only for MSK-IMPACT internal samples} \begin{Verbatim}[commandchars=\\\{\}] -\PYGZgt{} python iCallSV\PYGZus{}dmp\PYGZus{}wrapper.py \PYGZhy{}h +python iCallSV\PYGZus{}dmp\PYGZus{}wrapper.py \PYGZhy{}h usage: iCallSV\PYGZus{}dmp\PYGZus{}wrapper.py \PYG{o}{[}options\PYG{o}{]} @@ -429,9 +432,55 @@ \section{Utilities} \end{Verbatim} +\subsection{Taking the iCallSV and chechking for processed transcript/cDNA in samples} +\label{iCallSV:taking-the-icallsv-and-chechking-for-processed-transcript-cdna-in-samples} +\begin{Verbatim}[commandchars=\\\{\}] +python check\PYGZus{}cDNA\PYGZus{}contamination.py \PYGZhy{}h +usage: check\PYGZus{}cDNA\PYGZus{}contamination.py \PYG{o}{[}options\PYG{o}{]} + +Calculate cDNA contamination per sample based of the Structural Variants +Pipeline result + +optional arguments: + \PYGZhy{}h, \PYGZhy{}\PYGZhy{}help show this \PYG{n+nb}{help} message and \PYG{n+nb}{exit} + \PYGZhy{}v, \PYGZhy{}\PYGZhy{}verbose make lots of noise \PYG{o}{[}default\PYG{o}{]} + \PYGZhy{}s SVfile.txt, \PYGZhy{}\PYGZhy{}svFile SVfile.txt + Location of the structural variant file to be used + \PYGZhy{}o cDNA\PYGZus{}contamination, \PYGZhy{}\PYGZhy{}outputFileName cDNA\PYGZus{}contamination + Full path name \PYG{k}{for} the output file +\end{Verbatim} + + \section{Submodules} \label{iCallSV:submodules} +\subsection{iCallSV.iCallSV module} +\label{iCallSV:icallsv-icallsv-module}\label{iCallSV:module-iCallSV.iCallSV}\index{iCallSV.iCallSV (module)} + +\subsubsection{iCallSV} +\label{iCallSV:icallsv}\begin{quote}\begin{description} +\item[{Description}] \leavevmode +iCallSV is a wrapper to the iCallSV package which facilitates calling structural variants from Next Generation Sequencing methods such as Illumina + +\item[{author}] \leavevmode +Ronak H Shah + +\item[{copyright}] \leavevmode\begin{enumerate} +\setcounter{enumi}{2} +\item {} +2015-2016 by Ronak H Shah for Memorial Sloan Kettering Cancer Center. All rights reserved. + +\end{enumerate} + +\item[{license}] \leavevmode +Apache License 2.0 + +\item[{contact}] \leavevmode +\href{mailto:rons.shah@gmail.com}{rons.shah@gmail.com} + +\end{description}\end{quote} + + \subsection{iCallSV.FilterDellyCalls module} \label{iCallSV:icallsv-filterdellycalls-module}\label{iCallSV:module-iCallSV.FilterDellyCalls}\index{iCallSV.FilterDellyCalls (module)} @@ -1337,215 +1386,11 @@ \subsubsection{filterAnnotatedSV} -\subsection{iCallSV.iCallSV module} -\label{iCallSV:icallsv-icallsv-module}\label{iCallSV:module-iCallSV.iCallSV}\index{iCallSV.iCallSV (module)} - -\subsubsection{iCallSV} -\label{iCallSV:icallsv}\begin{quote}\begin{description} -\item[{Description}] \leavevmode -iCallSV is a wrapper to the iCallSV package which facilitates calling structural variants from Next Generation Sequencing methods such as Illumina - -\item[{author}] \leavevmode -Ronak H Shah - -\item[{copyright}] \leavevmode\begin{enumerate} -\setcounter{enumi}{2} -\item {} -2015-2016 by Ronak H Shah for Memorial Sloan Kettering Cancer Center. All rights reserved. - -\end{enumerate} - -\item[{license}] \leavevmode -Apache License 2.0 - -\item[{contact}] \leavevmode -\href{mailto:rons.shah@gmail.com}{rons.shah@gmail.com} - -\end{description}\end{quote} - - -\subsection{iCallSV.iCallSV\_dmp\_wrapper module} -\label{iCallSV:icallsv-icallsv-dmp-wrapper-module}\label{iCallSV:module-iCallSV.iCallSV_dmp_wrapper}\index{iCallSV.iCallSV\_dmp\_wrapper (module)} - -\subsubsection{iCallSV\_dmp\_wrapper} -\label{iCallSV:icallsv-dmp-wrapper}\begin{quote}\begin{description} -\item[{Description}] \leavevmode -iCallSV is a wrapper to run the iCallSV package on MSKCC data - -\item[{author}] \leavevmode -Ronak H Shah - -\item[{copyright}] \leavevmode\begin{enumerate} -\setcounter{enumi}{2} -\item {} -2015-2016 by Ronak H Shah for Memorial Sloan Kettering Cancer Center. All rights reserved. - -\end{enumerate} - -\item[{license}] \leavevmode -Apache License 2.0 - -\item[{contact}] \leavevmode -\href{mailto:rons.shah@gmail.com}{rons.shah@gmail.com} - -\item[{deffield updated}] \leavevmode -Updated - -\end{description}\end{quote} -\index{RunJob() (in module iCallSV.iCallSV\_dmp\_wrapper)} - -\begin{fulllineitems} -\phantomsection\label{iCallSV:iCallSV.iCallSV_dmp_wrapper.RunJob}\pysiglinewithargsret{\code{iCallSV.iCallSV\_dmp\_wrapper.}\bfcode{RunJob}}{\emph{cmd}}{} -Given a command run the job. -\begin{quote}\begin{description} -\item[{Parameters}] \leavevmode -\textbf{\texttt{cmd}} (\emph{\texttt{str}}) -- str of command to be run on the local machine - -\item[{Returns}] \leavevmode -None - -\item[{Return type}] \leavevmode -None - -\end{description}\end{quote} - -\end{fulllineitems} - -\index{RunPerPool() (in module iCallSV.iCallSV\_dmp\_wrapper)} - -\begin{fulllineitems} -\phantomsection\label{iCallSV:iCallSV.iCallSV_dmp_wrapper.RunPerPool}\pysiglinewithargsret{\code{iCallSV.iCallSV\_dmp\_wrapper.}\bfcode{RunPerPool}}{\emph{titleFile}, \emph{outdir}, \emph{HSmetricsFileList}, \emph{bamFileList}, \emph{args}}{} -This will run the pool to be analyzed. -\begin{quote}\begin{description} -\item[{Parameters}] \leavevmode\begin{itemize} -\item {} -\textbf{\texttt{titleFile}} (\emph{\texttt{str}}) -- str of meta information file - -\item {} -\textbf{\texttt{outdir}} (\emph{\texttt{str}}) -- str of output directory - -\item {} -\textbf{\texttt{HSmetricsFileList}} (\emph{\texttt{list}}) -- list of picard hsmetrics files - -\item {} -\textbf{\texttt{bamFileList}} (\emph{\texttt{list}}) -- list of bam files - -\item {} -\textbf{\texttt{args}} (\emph{\texttt{Namespace}}) -- Namespace of args to get other variables - -\end{itemize} - -\item[{Returns}] \leavevmode -None - -\item[{Return type}] \leavevmode -None - -\end{description}\end{quote} - -\end{fulllineitems} - -\index{SelectNormal() (in module iCallSV.iCallSV\_dmp\_wrapper)} - -\begin{fulllineitems} -\phantomsection\label{iCallSV:iCallSV.iCallSV_dmp_wrapper.SelectNormal}\pysiglinewithargsret{\code{iCallSV.iCallSV\_dmp\_wrapper.}\bfcode{SelectNormal}}{\emph{normal}, \emph{poolnormal}}{} -Select the best possible normal. -\begin{quote}\begin{description} -\item[{Parameters}] \leavevmode\begin{itemize} -\item {} -\textbf{\texttt{normal}} (\emph{\texttt{str}}) -- str of match normal - -\item {} -\textbf{\texttt{poolnormal}} (\emph{\texttt{str}}) -- str of pool normal - -\end{itemize} - -\item[{Returns}] \leavevmode -str with decision whether to run matched or unmatched - -\item[{Return type}] \leavevmode -str - -\end{description}\end{quote} - -\end{fulllineitems} - -\index{SetupRun() (in module iCallSV.iCallSV\_dmp\_wrapper)} - -\begin{fulllineitems} -\phantomsection\label{iCallSV:iCallSV.iCallSV_dmp_wrapper.SetupRun}\pysiglinewithargsret{\code{iCallSV.iCallSV\_dmp\_wrapper.}\bfcode{SetupRun}}{\emph{poolName}, \emph{args}}{} -This will setup the run to be analyzed. -\begin{quote}\begin{description} -\item[{Parameters}] \leavevmode\begin{itemize} -\item {} -\textbf{\texttt{poolName}} (\emph{\texttt{str}}) -- str of pool to be analyzed - -\item {} -\textbf{\texttt{args}} (\emph{\texttt{Namespace}}) -- Namespace of args to get other variables - -\end{itemize} - -\item[{Returns}] \leavevmode -Multiple objects - -\item[{Return type}] \leavevmode -list - -\end{description}\end{quote} - -\end{fulllineitems} - -\index{getSubDirs() (in module iCallSV.iCallSV\_dmp\_wrapper)} - -\begin{fulllineitems} -\phantomsection\label{iCallSV:iCallSV.iCallSV_dmp_wrapper.getSubDirs}\pysiglinewithargsret{\code{iCallSV.iCallSV\_dmp\_wrapper.}\bfcode{getSubDirs}}{\emph{dirLocation}}{} -Get all sub directories. -\begin{quote}\begin{description} -\item[{Parameters}] \leavevmode -\textbf{\texttt{dirLocation}} (\emph{\texttt{str}}) -- str of directory location - -\item[{Returns}] \leavevmode -list of all sub directories - -\item[{Return type}] \leavevmode -list - -\end{description}\end{quote} - -\end{fulllineitems} - -\index{main() (in module iCallSV.iCallSV\_dmp\_wrapper)} - -\begin{fulllineitems} -\phantomsection\label{iCallSV:iCallSV.iCallSV_dmp_wrapper.main}\pysiglinewithargsret{\code{iCallSV.iCallSV\_dmp\_wrapper.}\bfcode{main}}{}{} -\end{fulllineitems} - -\index{processor() (in module iCallSV.iCallSV\_dmp\_wrapper)} - -\begin{fulllineitems} -\phantomsection\label{iCallSV:iCallSV.iCallSV_dmp_wrapper.processor}\pysiglinewithargsret{\code{iCallSV.iCallSV\_dmp\_wrapper.}\bfcode{processor}}{\emph{i}, \emph{jobqueue}}{} -Operate on a jobqueue. -\begin{quote}\begin{description} -\item[{Parameters}] \leavevmode\begin{itemize} -\item {} -\textbf{\texttt{i}} (\emph{\texttt{int}}) -- count of the job - -\item {} -\textbf{\texttt{jobqueue}} (\emph{\texttt{Namespace}}) -- Namespace for jobqueue - -\end{itemize} - -\item[{Returns}] \leavevmode -None - -\item[{Return type}] \leavevmode -None - -\end{description}\end{quote} - -\end{fulllineitems} - +\subsection{iCallSV.utilities.iCallSV\_dmp\_wrapper module} +\label{iCallSV:icallsv-utilities-icallsv-dmp-wrapper-module} +\subsection{iCallSV.utilities.check\_cDNA\_contamination module} +\label{iCallSV:icallsv-utilities-check-cdna-contamination-module} \subsection{iCallSV.launchThreads module} \label{iCallSV:icallsv-launchthreads-module}\label{iCallSV:module-iCallSV.launchThreads}\index{iCallSV.launchThreads (module)} @@ -1840,7 +1685,6 @@ \chapter{Indices and tables} \item {\texttt{iCallSV.filterAnnotatedSV}}, \pageref{iCallSV:module-iCallSV.filterAnnotatedSV} \item {\texttt{iCallSV.FilterDellyCalls}}, \pageref{iCallSV:module-iCallSV.FilterDellyCalls} \item {\texttt{iCallSV.iCallSV}}, \pageref{iCallSV:module-iCallSV.iCallSV} -\item {\texttt{iCallSV.iCallSV\_dmp\_wrapper}}, \pageref{iCallSV:module-iCallSV.iCallSV_dmp_wrapper} \item {\texttt{iCallSV.launch\_FilterDellyCalls}}, \pageref{iCallSV:module-iCallSV.launch_FilterDellyCalls} \item {\texttt{iCallSV.launch\_Run\_Delly}}, \pageref{iCallSV:module-iCallSV.launch_Run_Delly} \item {\texttt{iCallSV.launchThreads}}, \pageref{iCallSV:module-iCallSV.launchThreads} diff --git a/docs/iCallSV.rst b/docs/iCallSV.rst index 210668a..8b8d8a8 100644 --- a/docs/iCallSV.rst +++ b/docs/iCallSV.rst @@ -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: diff --git a/iCallSV/configuration/template.ini b/iCallSV/configuration/template.ini index d16a967..50307c2 100644 --- a/iCallSV/configuration/template.ini +++ b/iCallSV/configuration/template.ini @@ -1,25 +1,34 @@ -#Template configuration file to run iCallSV +#~~~Template configuration file to run iCallSV~~~# +#### Path to python executable ### [Python] PYTHON: +#### Path to R executable and R Lib ### [R] -RHOME: -RLIB: +RHOME: +RLIB: +#### Path to delly, bcftools executables and Version of delly (supports only 0.7.3)### [SVcaller] DELLY: DellyVersion: BCFTOOLS: +#### Path to hg19 Referece Fasta file ### [ReferenceFasta] REFFASTA: +#### Path to file containing regions to exclude please follow Delly documentation for this ### [ExcludeRegion] EXREGIONS: +#### Path to file containing regions to where lenient threshold will be used; and file containing genes to keep ### [HotSpotRegions] HotspotFile: GenesToKeep: +#### Path to file containing regions/genes to filter ### [BlackListRegions] BlackListFile: BlackListGenes: +#### Path to samtools executable ### [SAMTOOLS] SAMTOOLS: +#### Path to iAnnotateSV.py and all its required files, please follow iAnnotateSV documentation ### [iAnnotateSV] ANNOSV: GENOMEBUILD: @@ -29,10 +38,12 @@ UNIPROTFILE: CosmicCensus: RepeatRegionAnnotation: DGvAnnotations: +#### TargetSeqView Parameters ### [TargetSeqView] CalculateConfidenceScore: GENOMEBUILD: ReadLength: +#### Parameters to run Delly ### [ParametersToRunDelly] MAPQ: 20 NumberOfProcessors: 4 @@ -44,9 +55,9 @@ CaseCoverageHotspot = 5 ####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 ### @@ -66,16 +77,16 @@ CaseSupportingReadsHotspot: 1 ###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### OverallMapq: 20 ###Overall Mapping Quality Threshold Hotspot### -OverallMapqHotspot: 5 +OverallMapqHotspot: 5 \ No newline at end of file diff --git a/iCallSV/utilities/check_cDNA_contamination.py b/iCallSV/utilities/check_cDNA_contamination.py new file mode 100755 index 0000000..43a3965 --- /dev/null +++ b/iCallSV/utilities/check_cDNA_contamination.py @@ -0,0 +1,116 @@ +""" +Created on 11/01/2015. +@author: Ronak H Shah +###Required Input columns in the structural variant file +TumorId NormalId Chr1 Pos1 Chr2 Pos2 SV_Type Gene1 Gene2 Transcript1 Transcript2 Site1Description Site2Description Fusion Confidence Comments Connection_Type SV_LENGTH MAPQ PairEndReadSupport SplitReadSupport BrkptType ConsensusSequence TumorVariantCount TumorSplitVariantCount TumorReadCount TumorGenotypeQScore NormalVariantCount NormalSplitVariantCount NormalReadCount NormalGenotypeQScore +###Output columns +"TumorId Genes_with_cDNA_contamination" +""" + +import argparse +import pandas as pd +import time +import sys + +def main(): + parser = argparse.ArgumentParser( + prog='check_cDNA_contamination.py', + description='Calculate cDNA contamination per sample based of the Structural Variants Pipeline result', + usage='%(prog)s [options]') + parser.add_argument( + "-v", + "--verbose", + action="store_true", + dest="verbose", + default=True, + help="make lots of noise [default]") + parser.add_argument( + "-s", + "--svFile", + action="store", + dest="svFilename", + required=True, + metavar='SVfile.txt', + help="Location of the structural variant file to be used") + parser.add_argument( + "-o", + "--outputFileName", + action="store", + dest="outFileName", + required=True, + metavar='cDNA_contamination', + help="Full path name for the output file") + args = parser.parse_args() + # Read the structural variant file + (dataDF) = ReadSV(args.svFilename, args) + # Process the structural variant file + (dataDict) = ProcessData(dataDF) + # Write results in the output file specified + WriteResults(dataDict, args) +# Read the structural variant file +def ReadSV(file, args): + dataDF = pd.read_csv(file, sep='\t', header=0, keep_default_na='True') + return(dataDF) +# Process the pandas dataframe to get contaminataed genes +def ProcessData(dataDF): + # Group the data by tumor id, gene1 name, type of sv + gDF = dataDF.groupby(['TumorId', 'Gene1', 'SV_Type']).groups + # initialize and empty dictionary + resultdict = {} + # traverse through gDF dictionary + for key, value in gDF.iteritems(): + # get name of the sample its meta data + (tumorID, gene1, svtype) = key + # check how many entries are there of sv type + entires = len(value) + # initialize the number of cDNA events and a list of corresponding genes + count = 0 + geneList = [] + # run only if the event is deletion and has more then 2 entries for the same gene + if(svtype == 'DEL' and entires >= 2): + for idx in value: + record = dataDF.loc[idx] + site1 = str(record.loc['Site1Description']) + site2 = str(record.loc['Site2Description']) + fusion = str(record.loc['Fusion']) + brkptType = str(record.loc['BrkptType']) + # Skip entries that are within exon or are in-frame or out-of frame or are IMPRECISE. + if(("Exon" in site1 and "Exon" in site2) or ("in frame" in fusion or "out of frame" in fusion) or (brkptType == "IMPRECISE")): + continue + else: + count = count + 1 + # count the entries,genes and fill the resultdict + if tumorID in resultdict: + geneList = resultdict[tumorID] + if(count >= 2): + geneList.append(gene1) + resultdict[tumorID] = geneList + else: + if(count >= 2): + geneList.append(gene1) + resultdict[tumorID] = geneList + return(resultdict) + +def WriteResults(dataDict, args): + if not dataDict: + print "No contamination found\n" + return() + else: + # Convert the dictionaries values which are as list to string + for key, value in dataDict.iteritems(): + newvalue = ', '.join(value) + dataDict[key] = newvalue + + resultDF = pd.DataFrame(dataDict.items(), columns=['TumorId', 'Genes_with_cDNA_contamination']).sort('TumorId') + # Print to TSV file + resultDF.to_csv(args.outFileName, sep='\t', index=False) + return() + +#Run the main program +if __name__ == "__main__": + start_time = time.time() + main() + end_time = time.time() + seconds = end_time - start_time + print "Elapsed time was ", time.strftime("%H:%M:%S", time.gmtime(seconds)) + \ No newline at end of file diff --git a/iCallSV/iCallSV_dmp_wrapper.py b/iCallSV/utilities/iCallSV_dmp_wrapper.py similarity index 100% rename from iCallSV/iCallSV_dmp_wrapper.py rename to iCallSV/utilities/iCallSV_dmp_wrapper.py