Merge branch 'release/1.2.0'

.github/workflows/python-package.yml

@@ -0,0 +1,39 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [2.7.15]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with nosetest
+      run: |
+        nosetests -v --with-coverage --cover-tests tests

.gitignore

@@ -86,4 +86,8 @@ ENV/
 .spyderproject
 
 # Rope project settings
-.ropeproject
+.ropeproject
+
+# IDE settings
+.vscode/
+.idea/

.travis.yml

@@ -1,7 +1,19 @@
 language: python
 python:
-  - "2.7.10"
+  - "2.7.15"
 # command to install dependencies
 install: "pip install -r requirements.txt"
 # command to run tests
 script: nosetests -v --with-coverage
+deploy:
+  provider: pypi
+  distributions: sdist bdist_wheel
+  skip_cleanup: true
+  skip_existing: true
+  user: __token__
+  password:
+    secure: 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
+  on:
+    tags: true
+    repo: rhshah/iAnnotateSV
+    python: 2.7.15

CHANGES.rst

@@ -20,4 +20,6 @@ Updated to have no padding and proper transcript selection
 v1.0.8
 Removing TIMM23B for proper annotation of RET-NCOA4
 v1.0.9
-RS:Added funtionality to kinase domain involvement in the annotation
+RS:Added functionality to kinase domain involvement in the annotation
+v1.2.0
+RS:Bug fix for running auto selection mode and upgrading requirements

README.rst

@@ -38,17 +38,19 @@ If you use this software in a publication, for now, please cite our website `iAn
 Acknowledgements
 ================
 
-I would like to thanks Mike Lawrence from Broad Institue for sharing his code and Michael Berger for his insights into the dRanger_annotate tool.
+I would like to thanks Mike Lawrence from Broad Institute for sharing his code and Michael Berger for his insights into the dRanger_annotate tool.
 
 Required Packages
 =================
 We require that you install:
 
+:python: `v2.7.15 <https://www.python.org/downloads/release/python-2715/>`_
 :pandas: `v0.24.2 <http://pandas.pydata.org/>`_
-:biopython: `v1.65 <http://biopython.org/wiki/Main_Page>`_
-:Pillow: `v3.4.2 <https://pypi.python.org/pypi/Pillow/3.4.2>`_
-:reportlab: `v3.3.0 <https://pypi.python.org/pypi/reportlab/3.3.0>`_
-:coloredlogs: `v5.2 <https://pypi.python.org/pypi/coloredlogs>`_
+:biopython: `v1.76 <http://biopython.org/wiki/Main_Page>`_
+:Pillow: `v6.2.1 <https://pypi.python.org/pypi/Pillow/3.4.2>`_
+:openpyxl: `v2.6.4 <https://pypi.python.org/pypi/openpyxl/2.6.4>`_
+:reportlab: `v3.5.2 <https://pypi.python.org/pypi/reportlab/3.5.2>`_
+:coloredlogs: `v14.0 <https://pypi.python.org/pypi/coloredlogs>`_
 
 Quick Usage
 ===========
@@ -64,7 +66,7 @@ Else To Run:
 
             ``python path/to/path/to/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 (making plots is a test module only):
 
             ``python path/to/iAnnotateSV.py -i svFile.txt -ofp outputfilePrefix -o /path/to/output/dir -r hg19 -d 3000 -c canonicalTranscripts.txt -u uniprot.txt -p``
 
@@ -95,7 +97,7 @@ Else To Run:
                             Location of canonical transcript list for each gene.
                             Use only if you want the output for specific
                             transcripts for each gene.
-    -p, --plotSV          Plot the structural variant in question
+    -p, --plotSV          Plot the structural variant in question (very primitive)
     -u uniprot.txt, --uniprotFile uniprot.txt
                             Location of UniProt list contain information for
                             protein domains. Use only if you want to plot the

docs/conf.py

@@ -51,9 +51,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.0.1'
+version = '1.2.0'
 # The full version, including alpha/beta/rc tags.
-release = '0.0.1'
+release = '1.2.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/iAnnotateSV.rst

@@ -6,11 +6,13 @@ Required Packages
 
 We require that you install:
 
-:pandas: `v0.16.2 <http://pandas.pydata.org/>`_
-:biopython: `v1.65 <http://biopython.org/wiki/Main_Page>`_
-:Pillow: `v3.4.2 <https://pypi.python.org/pypi/Pillow/3.4.2>`_
-:reportlab: `v3.3.0 <https://pypi.python.org/pypi/reportlab/3.3.0>`_
-:coloredlogs: `v5.2 <https://pypi.python.org/pypi/coloredlogs>`_
+:python: `v2.7.15 <https://www.python.org/downloads/release/python-2715/>`_
+:pandas: `v0.24.2 <http://pandas.pydata.org/>`_
+:biopython: `v1.76 <http://biopython.org/wiki/Main_Page>`_
+:Pillow: `v6.2.1 <https://pypi.python.org/pypi/Pillow/3.4.2>`_
+:openpyxl: `v2.6.4 <https://pypi.python.org/pypi/openpyxl/2.6.4>`_
+:reportlab: `v3.5.2 <https://pypi.python.org/pypi/reportlab/3.5.2>`_
+:coloredlogs: `v14.0 <https://pypi.python.org/pypi/coloredlogs>`_
 
 Quick Usage
 ===========
@@ -26,7 +28,7 @@ Else To Run:
 
             ``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``
 

docs/index.rst

@@ -51,7 +51,7 @@ If you use this software in a publication, for now, please cite our website `iAn
 Acknowledgements
 ================
 
-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.
+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
 ==================