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Index

\ No newline at end of file diff --git a/docs/_build/html/iAnnotateSV.html b/docs/_build/html/iAnnotateSV.html index 76feda7..c1b3b4a 100644 --- a/docs/_build/html/iAnnotateSV.html +++ b/docs/_build/html/iAnnotateSV.html @@ -4,28 +4,20 @@ + - iAnnotateSV package — iAnnotateSV 0.0.1 documentation + iAnnotateSV package — iAnnotateSV 1.2.0 documentation - + + - - + @@ -55,15 +47,19 @@

Required Packages -pandas:v0.16.2 +python:v2.7.15 -biopython:v1.65 +pandas:v0.24.2 -Pillow:v3.4.2 +biopython:v1.76 -reportlab:v3.3.0 +Pillow:v6.2.1 -coloredlogs:v5.2 +openpyxl:v2.6.4 + +reportlab:v3.5.2 + +coloredlogs:v14.0 @@ -76,18 +72,18 @@

Quick Usage
  • If you want to run with default options:
    • -

    python iAnnotateSV.py -i svFile.txt -ofp outputfilePrefix -o /path/to/output/dir -r hg19 -d 3000

    +

    python iAnnotateSV.py -i svFile.txt -ofp outputfilePrefix -o /path/to/output/dir -r hg19 -d 3000

    • If you want to run with your own transcripts:
    -

    python iAnnotateSV.py -i svFile.txt -ofp outputfilePrefix -o /path/to/output/dir -r hg19 -d 3000 -c canonicalTranscripts.txt

    +

    python iAnnotateSV.py -i svFile.txt -ofp outputfilePrefix -o /path/to/output/dir -r hg19 -d 3000 -c canonicalTranscripts.txt

      -
    • If you want to run with your own transcripts & make plots:
      • +
    • If you want to run with your own transcripts & make plots (plot making is a test functionality):
    -

    python iAnnotateSV.py -i svFile.txt -ofp outputfilePrefix -o /path/to/output/dir -r hg19 -d 3000 -c canonicalTranscripts.txt -u uniprot.txt -p

    +

    python iAnnotateSV.py -i svFile.txt -ofp outputfilePrefix -o /path/to/output/dir -r hg19 -d 3000 -c canonicalTranscripts.txt -u uniprot.txt -p

    -
    usage: iAnnotateSV.py [options]
+
    usage: iAnnotateSV.py [options]
 
 **Annotate SV based on a specific human reference**
 
@@ -227,13 +223,13 @@ 
    Quick Usage
-
    Module iAnnotateSV contents
    
+
    Module iAnnotateSV contents
    
 
    
 
    
 
    Submodules
    
 
    
 
    
-
    AnnotateEachBreakpoint module
    
+
    AnnotateEachBreakpoint module
    
 
      
 
    • 
 
      This module will annotate each breakpoint taking in:
      
@@ -247,7 +243,7 @@ 
      AnnotateEachBreakpoint
 
 
-Example:AnnotateEachBreakpoint(chr1,pos1,str1,refDF)
+Example:AnnotateEachBreakpoint(chr1,pos1,str1,refDF)
 
 
 
@@ -257,7 +253,7 @@ 
      AnnotateEachBreakpoint
 
    
 
    
-
    FindATranscript module
    
+
    FindATranscript module
    
 
      
 
    • 
 
      This module will automatically find the highest preference transcript based on input:
      
@@ -279,7 +275,7 @@ 
      FindATranscript
 
 
-Example:FindATranscript(queryDF,refDF)
+Example:FindATranscript(queryDF,refDF)
 
 
 
@@ -289,7 +285,7 @@ 
      FindATranscript
 
    
 
    
-
    FindAllTranscripts module
    
+
    FindAllTranscripts module
    
 
      
 
    • 
 
      This module will find all transcripts based on input:
      
@@ -311,7 +307,7 @@ 
      FindAllTranscripts
 
 
-Example:FindAllTranscripts(queryDF,refDF)
+Example:FindAllTranscripts(queryDF,refDF)
 
 
 
@@ -321,7 +317,7 @@ 
      FindAllTranscripts
 
    
 
    
-
    FindCanonicalTranscript module
    
+
    FindCanonicalTranscript module
    
 
      
 
    • 
 
      This module will Finad a canonical transcript based on the input for main function and output of FindAllTranscripts:
      
@@ -339,7 +335,7 @@ 
      FindCanonicalTranscript
 
 
-Example:FindCT(geneList,transcriptList,siteList,zoneList,strandList,intronnumList,intronframeList,ctDict)
+Example:FindCT(geneList,transcriptList,siteList,zoneList,strandList,intronnumList,intronframeList,ctDict)
 
 
 
@@ -349,7 +345,7 @@ 
      FindCanonicalTranscript
 
    
 
    
-
    PredictFunction module
    
+
    PredictFunction module
    
 
      
 
    • This module will predict the function of each annotated breakpoint
      
 
      • 
@@ -369,10 +365,10 @@ 
      PredictFunction
 
 
-Example:
      ann1S = pandas.Series([gene1,transcript1,site1,zone1,strand1,str1,intronnum1,intronframe1],index=['gene1', 'transcript1', 'site1', 'zone1', 'txstrand1', 'readstrand1', 'intronnum1','intronframe1'])
      
-
      ann2S = pandas.Series([gene2,transcript2,site2,zone2,strand2,str2,intronnum2,intronframe2],index=['gene2', 'transcript2', 'site2', 'zone2', 'txstrand2', 'readstrand2', 'intronnum2','intronframe2'])
      
+Example:
      ann1S = pandas.Series([gene1,transcript1,site1,zone1,strand1,str1,intronnum1,intronframe1],index=['gene1', 'transcript1', 'site1', 'zone1', 'txstrand1', 'readstrand1', 'intronnum1','intronframe1'])
      
+
      ann2S = pandas.Series([gene2,transcript2,site2,zone2,strand2,str2,intronnum2,intronframe2],index=['gene2', 'transcript2', 'site2', 'zone2', 'txstrand2', 'readstrand2', 'intronnum2','intronframe2'])
      
 
      So ann1S & ann2S are series that will go to PredictFuntionForSV()
      
-
      PredictFunctionForSV(ann1S,ann2S)
      
+
      PredictFunctionForSV(ann1S,ann2S)
      
 
 
 
@@ -383,15 +379,15 @@ 
      PredictFunction
 
    
 
    
-
    AddExternalAnnotations module
    
+
    AddExternalAnnotations module
    
 
      
 
    • 
 
      This module will annotate each breakpoint for Repeat Region, Database of Genomic Variants and Cosmic Census taking in:
      
 
        
-
      • repeat region file : Repeat Track from UCSC in tab-delimited format (see: /data/repeat_region/hg19_repeatRegion.tsv),
        • 
-
      • data base of genimic variant file : DGv in tab-delimited format (see: /data/database_of_genomic_variants/hg19_DGv_Annotation.tsv),
        • 
-
      • cosmic census file : cosmic census file from sanger (see: /data/cosmic/cancer_gene_census.tsv),
        • 
-
      • cosmic fusion counts file : cosmic fusion counts file from from cosmic fusion export (see: /data/cosmic/cosmic_fusion_counts.tsv),
        • 
+
      • repeat region file : Repeat Track from UCSC in tab-delimited format (see: /data/repeat_region/hg19_repeatRegion.tsv),
        • 
+
      • data base of genimic variant file : DGv in tab-delimited format (see: /data/database_of_genomic_variants/hg19_DGv_Annotation.tsv),
        • 
+
      • cosmic census file : cosmic census file from sanger (see: /data/cosmic/cancer_gene_census.tsv),
        • 
+
      • cosmic fusion counts file : cosmic fusion counts file from from cosmic fusion export (see: /data/cosmic/cosmic_fusion_counts.tsv),
        • 
 
      • structural variants file : File containing the breakpoint information,
        • 
 
      • output prefix : Output Prefix for the output files (.xlsx,.json,.txt),
        • 
 
      • output directory : Directory where the output needs to be written
        • 
@@ -400,8 +396,8 @@ 
        AddExternalAnnotations
 
 
-Example:
        makeCommandLineForAEA = "-r " + repeatregionFilePath + " -d " + dgvFilePath + " -c " + ccFilePath + " -cct " + cctFilePath + " -s " + svFilePath + " -ofp AnnotatedSV" + " -o " + outputDir
        
-
        AddExternalAnnotations.main(makeCommandLineForAEA)
        
+Example:
        makeCommandLineForAEA = "-r " + repeatregionFilePath + " -d " + dgvFilePath + " -c " + ccFilePath + " -cct " + cctFilePath + " -s " + svFilePath + " -ofp AnnotatedSV" + " -o " + outputDir
        
+
        AddExternalAnnotations.main(makeCommandLineForAEA)
        
 
 
 
@@ -412,7 +408,7 @@ 
        AddExternalAnnotations
 
    
 
    
-
    AnnotateForRepeatRegion module
    
+
    AnnotateForRepeatRegion module
    
 
      
 
    • 
 
      This module has two submodules will read and annotate each breakpoint for Repeat Region
      
@@ -433,7 +429,7 @@ 
      AnnotateForRepeatRegion
 
 
-Example:AnnotateRepeatRegion(verbose, count, svObject, repeatregionDict)
+Example:AnnotateRepeatRegion(verbose, count, svObject, repeatregionDict)
 
 
 
@@ -446,7 +442,7 @@ 
      AnnotateForRepeatRegion
 
    
 
    
-
    AnnotateForDGv module
    
+
    AnnotateForDGv module
    
 
      
 
    • 
 
      This module has two submodules will read and annotate each breakpoint for Database of Genomic Variants
      
@@ -467,7 +463,7 @@ 
      AnnotateForDGv
 
 
-Example:AnnotateDGv(verbose, count, svObject, dgvDict)
+Example:AnnotateDGv(verbose, count, svObject, dgvDict)
 
 
 
@@ -480,7 +476,7 @@ 
      AnnotateForDGv
 
    
 
    
-
    AnnotateForCosmic module
    
+
    AnnotateForCosmic module
    
 
      
 
    • This module will annotate each breakpoint for Cosmic Census
      
 
      
@@ -488,9 +484,9 @@ 
      AnnotateForCosmic
 
 
-Example:AnnotateFromCosmicCensusFile(comic_census_filename, verbose, count, svObject)
+Example:AnnotateFromCosmicCensusFile(comic_census_filename, verbose, count, svObject)
 
-Example:AnnotateFromComicFusionCountsFile(comic_fusion_counts_filename, verbose, count, svObject)
+Example:AnnotateFromComicFusionCountsFile(comic_fusion_counts_filename, verbose, count, svObject)
 
 
 
@@ -499,7 +495,7 @@ 
      AnnotateForCosmic
 
    
 
    
-
    helper module
    
+
    helper module
    
 
      
 
    • 
 
      This module has multiple submodules
      
@@ -523,7 +519,7 @@ 
      helper module
 
    
 
    
 
    
-
    VisualizeSV module
    
+
    VisualizeSV module
    
 
      
 
    • 
 
      This module will annotate each breakpoint taking in:
      
@@ -537,7 +533,7 @@ 
      VisualizeSV m
 
 
 
-Example:
      VisualizeSV(svDataFrame,referenceDataFrame,uniprotDataFrame,args)
      
+Example:
      VisualizeSV(svDataFrame,referenceDataFrame,uniprotDataFrame,args)
      
 
 
 Example Plot:Image of EWSR1-ERG Fusion
@@ -551,11 +547,11 @@ 
      VisualizeSV m
 
    
 
    
 
    
-
    iAnnotateSV module
    
+
    iAnnotateSV module
    
 
      
 
    • This module is the driver module, it takes user information and runs all other module to produce proper structural variant annotation
      • 
 
    
-
    usage: iAnnotateSV.py [options]**
+
    usage: iAnnotateSV.py [options]**
 
 Annotate SV based on a specific human reference**
 
@@ -602,25 +598,25 @@ 
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-    iAnnotateSV: Annotation of structural variants detected from NGS — iAnnotateSV 0.0.1 documentation
+    iAnnotateSV: Annotation of structural variants detected from NGS — iAnnotateSV 1.2.0 documentation
     
     
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    Citation
 
    Acknowledgements
    
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    I would like to thanks Mike Lawrence from Braod Institue for sharing his code and Michael Berger for his inshgts into the dRanger_Annoate tool.
    
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    I would like to thanks Mike Lawrence from Broad Institute for sharing his code and Michael Berger for his inshgts into the dRanger_Annoate tool.
    
 
    
 
    
 
    Indices and tables
    
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-    iAnnotateSV — iAnnotateSV 0.0.1 documentation
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    iAnnotateSViAnnotateSV package
 
  • Required Packages
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  • Quick Usage
 
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    \ No newline at end of file diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv index faa7ecb..539214c 100644 Binary files a/docs/_build/html/objects.inv and b/docs/_build/html/objects.inv differ diff --git a/docs/_build/html/search.html b/docs/_build/html/search.html index 0e57074..60e613f 100644 --- a/docs/_build/html/search.html +++ b/docs/_build/html/search.html @@ -4,23 +4,17 @@ + - Search — iAnnotateSV 0.0.1 documentation + Search — iAnnotateSV 1.2.0 documentation - + + + @@ -31,15 +25,14 @@ - - + @@ -87,12 +80,12 @@

    Navigation

  • index
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    • \ No newline at end of file diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js index 9327ae0..f4ee46b 100644 --- a/docs/_build/html/searchindex.js +++ b/docs/_build/html/searchindex.js @@ -1 +1 @@ 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package","iAnnotateSV: Annotation of structural variants detected from NGS","iAnnotateSV"],titleterms:{NGS:1,acknowledg:1,addexternalannot:0,annot:1,annotateeachbreakpoint:0,annotateforcosm:0,annotatefordgv:0,annotateforrepeatregion:0,citat:1,content:0,detect:1,findalltranscript:0,findatranscript:0,findcanonicaltranscript:0,from:1,helper:0,iannotatesv:[0,1,2],indic:1,modul:0,packag:0,predictfunct:0,quick:0,requir:0,structur:1,submodul:0,tabl:1,usag:0,variant:1,visualizesv:0}}) \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index 54d4adf..83393fc 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -17,6 +17,9 @@ But it also has some additional functionality and control over the annotation w. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina. +.. image:: https://img.shields.io/pypi/v/iAnnotateSV.svg + :target: https://pypi.python.org/pypi/iAnnotateSV + .. image:: https://landscape.io/github/rhshah/iAnnotateSV/master/landscape.svg?style=flat :target: https://landscape.io/github/rhshah/iAnnotateSV/master diff --git a/setup.cfg b/setup.cfg index 1543f8d..19b7ff8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -12,7 +12,7 @@ classifiers = Operating System :: OS Independent Intended Audience :: Science/Research Topic :: Scientific/Engineering :: Bio-Informatics - Development Status :: 3 + Development Status :: 5 - Production/Stable [bumpversion] current_version = 1.2.0 diff --git a/setup.py b/setup.py index 656494e..65572d9 100755 --- a/setup.py +++ b/setup.py @@ -1,6 +1,6 @@ from __future__ import print_function try: - from setuptools import setup, find_packages + from setuptools import setup, find_packages, Extension except ImportError: from distutils.core import setup, find_packages import io @@ -21,16 +21,16 @@ def read(*filenames, **kwargs): buf.append(f.read()) return sep.join(buf) -long_description = read('README.rst', 'CHANGES.rst') +#long_description = read('README.rst', 'CHANGES.rst') setup( name='iAnnotateSV', version=iAnnotateSV.__version__, description='The module helps to annotate structural variants called using NGS on human.', - long_description=long_description, + long_description='See Readme', include_package_data=True, url='https://github.com/rhshah/iAnnotateSV', - download_url = 'https://github.com/rhshah/iAnnotateSV/tarball/1.1.1', + download_url = 'https://github.com/rhshah/iAnnotateSV/tarball/1.2.0', author=iAnnotateSV.__author__, author_email='rons.shah@gmail.com', license=iAnnotateSV.__license__, @@ -53,10 +53,10 @@ def read(*filenames, **kwargs): classifiers=( 'Programming Language :: Python', 'Programming Language :: Python :: 2.7', - 'License :: OSI Approved :: Apache License', + 'License :: OSI Approved :: Apache Software License', 'Operating System :: OS Independent', 'Intended Audience :: Science/Research', 'Topic :: Scientific/Engineering :: Bio-Informatics', - 'Development Status :: 3' + 'Development Status :: 5 - Production/Stable' ), )