Merge remote-tracking branch 'origin/master' into mhcflurry

griffithlab · Apr 15, 2020 · 9fed25f · 9fed25f
2 parents 3068175 + a032e72
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diff --git a/.travis.yml b/.travis.yml
@@ -23,10 +23,13 @@ matrix:
             - pip install tensorflow==1.14.0
             - pip install keras==2.2.5
             - pip install Werkzeug==0.16.1
+            - pip install coveralls
           services:
             - postgresql
           script:
-            - TEST_FLAG=1 python3 -m unittest discover -v
+            - TEST_FLAG=1 coverage run --source=lib,tools -m unittest discover -v
+          after_success:
+            - coveralls
         - name: "Python 3.6"
           language: python
           sudo: required
@@ -49,10 +52,13 @@ matrix:
             - pip install keras==2.2.5
             - pip install pandas==0.25.2
             - pip install Werkzeug==0.16.1
+            - pip install coveralls
           services:
             - postgresql
           script:
-            - TEST_FLAG=1 python3 -m unittest discover -v
+            - TEST_FLAG=1 coverage run --source=lib,tools -m unittest discover -v
+          after_success:
+            - coveralls
         - name: "Python 3.7"
           language: python
           sudo: required
@@ -75,7 +81,10 @@ matrix:
             - pip install keras==2.2.5
             - pip install pandas==0.25.2
             - pip install Werkzeug==0.16.1
+            - pip install coveralls
           services:
             - postgresql
           script:
-            - TEST_FLAG=1 python3 -m unittest discover -v
+            - TEST_FLAG=1 coverage run --source=lib,tools -m unittest discover -v
+          after_success:
+            - coveralls
diff --git a/README.md b/README.md
@@ -1,3 +1,10 @@
+[![Build Status](https://travis-ci.org/griffithlab/pVACtools.svg?branch=master)](https://travis-ci.org/griffithlab/pVACtools)
+[![Coverage Status](https://coveralls.io/repos/github/griffithlab/pVACtools/badge.svg?branch=master)](https://coveralls.io/github/griffithlab/pVACtools?branch=master)
+[![Docs](https://readthedocs.org/projects/pvactools/badge/?version=latest)](http://pvactools.readthedocs.io/en/latest/?badge=latest)
+<a href="https://pypi.python.org/pypi/pvactools/">
+    <img src="https://img.shields.io/pypi/v/pvactools.svg?maxAge=1000" alt="PyPI" />
+</a>
+
 # pVACtools
 
 pVACtools is a cancer immunotherapy suite consisting of the following tools:
@@ -26,8 +33,8 @@ A browser-based user interface that assists users in launching, managing, review
 
 The pVACapi provides a HTTP REST interface to the pVACtools suite.
 
-## Citation
-Jasreet Hundal, Susanna Kiwala, Joshua McMichael, Christopher A Miller, Alexander T Wollam, Huiming Xia, Connor J Liu, Sidi Zhao, Yang-Yang Feng, Aaron P Graubert, Amber Z Wollam, Jonas Neichin, Megan Neveau, Jason Walker, William E Gillanders, Elaine R Mardis, Obi L Griffith, Malachi Griffith. [pVACtools: a computational toolkit to select and visualize cancer neoantigens](https://doi.org/10.1101/501817). bioRxiv 501817; doi: https://doi.org/10.1101/501817
+## Citations
+Jasreet Hundal , Susanna Kiwala , Joshua McMichael, Chris Miller, Huiming Xia, Alex Wollam, Conner Liu, Sidi Zhao, Yang-Yang Feng, Aaron Graubert, Amber Wollam, Jonas Neichin, Megan Neveau, Jason Walker, William Gillanders, Elaine Mardis, Obi Griffith, Malachi Griffith. pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens. Cancer Immunology Research. 2020 Mar;8(3):409-420. doi: 10.1158/2326-6066.CIR-19-0401. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31907209">31907209</a>.
 
 Jasreet Hundal, Susanna Kiwala, Yang-Yang Feng, Connor J. Liu, Ramaswamy Govindan, William C. Chapman, Ravindra Uppaluri, S. Joshua Swamidass, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. <a href="https://doi.org/10.1038/s41588-018-0283-9">Accounting for proximal variants improves neoantigen prediction</a>. Nature Genetics. 2018, DOI: 10.1038/s41588-018-0283-9. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30510237">30510237</a>.
 
@@ -68,4 +75,13 @@ If you have an old version of pVACtools installed you might want to consider upg
 The pVACtools documentation can be found on <a href="http://pvactools.readthedocs.io/">ReadTheDocs</a>.
 
 ## Contact
+
 Bug reports or feature requests can be submitted on the <a href="https://github.com/griffithlab/pVACtools/issues">pVACtools Github page</a>. You may also contact us by email at help@pvactools.org.
+
+## Container images
+
+pVACtools is available as a Docker Image at <a href="https://hub.docker.com/r/griffithlab/pvactools/">DockerHub griffithlab/pvactools</a>.
+
+## Stable release with DOI
+
+[![DOI](https://zenodo.org/badge/102625109.svg)](https://zenodo.org/badge/latestdoi/102625109)
diff --git a/docs/index.rst b/docs/index.rst
@@ -140,22 +140,29 @@ To stay up-to-date on the latest pVACtools releases please join our :ref:`mailin
 Citations
 ---------
 
-Jasreet Hundal, Susanna Kiwala, Joshua McMichael, Christopher A Miller,
-Alexander T Wollam, Huiming Xia, Connor J Liu, Sidi Zhao, Yang-Yang Feng,
-Aaron P Graubert, Amber Z Wollam, Jonas Neichin, Megan Neveau, Jason Walker,
-William E Gillanders, Elaine R Mardis, Obi L Griffith, Malachi Griffith.
-`pVACtools: a computational toolkit to select and visualize cancer
-neoantigens <https://doi.org/10.1101/501817>`_.
-bioRxiv 501817; doi: https://doi.org/10.1101/501817
-
-Jasreet Hundal, Susanna Kiwala, Yang-Yang Feng, Connor J. Liu, Ramaswamy Govindan, William C. Chapman, Ravindra Uppaluri, S. Joshua Swamidass, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. `Accounting for proximal variants improves neoantigen prediction <https://www.nature.com/articles/s41588-018-0283-9>`_. Nature Genetics. 2018, DOI: 10.1038/s41588-018-0283-9. PMID: `30510237 <https://www.ncbi.nlm.nih.gov/pubmed/30510237>`_.
+Jasreet Hundal , Susanna Kiwala , Joshua McMichael, Chris Miller, Huiming Xia, 
+Alex Wollam, Conner Liu, Sidi Zhao, Yang-Yang Feng, Aaron Graubert, Amber Wollam, 
+Jonas Neichin, Megan Neveau, Jason Walker, William Gillanders,
+Elaine Mardis, Obi Griffith, Malachi Griffith. pVACtools: A Computational Toolkit to
+Identify and Visualize Cancer Neoantigens. Cancer Immunology Research. 
+2020 Mar;8(3):409-420. doi: 10.1158/2326-6066.CIR-19-0401. 
+PMID: `31907209 <https://www.ncbi.nlm.nih.gov/pubmed/31907209>`_.
+
+Jasreet Hundal, Susanna Kiwala, Yang-Yang Feng, Connor J. Liu, Ramaswamy Govindan, William C. Chapman, 
+Ravindra Uppaluri, S. Joshua Swamidass, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. 
+`Accounting for proximal variants improves neoantigen prediction <https://www.nature.com/articles/s41588-018-0283-9>`_. 
+Nature Genetics. 2018, DOI: 10.1038/s41588-018-0283-9. PMID: `30510237 <https://www.ncbi.nlm.nih.gov/pubmed/30510237>`_.
 
 Jasreet Hundal, Beatriz M. Carreno, Allegra A. Petti, Gerald P. Linette, Obi
 L. Griffith, Elaine R. Mardis, and Malachi Griffith. `pVACseq: A genome-guided
 in silico approach to identifying tumor neoantigens <http://www.genomemedicine.com/content/8/1/11>`_. Genome Medicine. 2016,
 8:11, DOI: 10.1186/s13073-016-0264-5. PMID: `26825632
 <http://www.ncbi.nlm.nih.gov/pubmed/26825632>`_.
 
+Source code
+-------
+The pVACtools source code is available in `GitHub <https://github.com/griffithlab/pVACtools>`_.
+
 License
 -------
 This project is licensed under `NPOSL-3.0 <http://opensource.org/licenses/NPOSL-3.0>`_.
diff --git a/tests/test_pvacfuse.py b/tests/test_pvacfuse.py
@@ -14,6 +14,8 @@
 from tools.pvacfuse import *
 from mock import patch
 from .test_utils import *
+import tools.pvacfuse.main as pvacfuse_main
+import argparse
 
 def make_response(data, files, path):
     if not files:
@@ -96,6 +98,10 @@ def test_pvacfuse_compiles(self):
         ))
         self.assertTrue(compiled_pvac_path)
 
+    def test_parser(self):
+        parser = pvacfuse_main.define_parser()
+        self.assertEqual(type(parser), argparse.ArgumentParser)
+
     def test_pvacfuse_commands(self):
         pvac_script_path = os.path.join(
             self.pVac_directory,
@@ -106,9 +112,11 @@ def test_pvacfuse_commands(self):
         usage_search = re.compile(r"usage: ")
         for command in [
             "run",
+            "allele_specific_cutoffs",
             "binding_filter",
             "valid_alleles",
             "download_example_data",
+            "top_score_filter",
             ]:
             result = subprocess_run([
                 sys.executable,
@@ -128,6 +136,71 @@ def test_run_compiles(self):
         ))
         self.assertTrue(compiled_run_path)
 
+    def test_allele_specific_cutoffs_compiles(self):
+        compiled_run_path = py_compile.compile(os.path.join(
+            self.pVac_directory,
+            "tools",
+            "pvacfuse",
+            "allele_specific_cutoffs.py"
+        ))
+        self.assertTrue(compiled_run_path)
+
+    def test_allele_specific_cutoffs_runs(self):
+        allele_specific_cutoffs.main([])
+
+    def test_binding_filter_compiles(self):
+        compiled_run_path = py_compile.compile(os.path.join(
+            self.pVac_directory,
+            "tools",
+            "pvacfuse",
+            "binding_filter.py"
+        ))
+        self.assertTrue(compiled_run_path)
+
+    def test_binding_filter_runs(self):
+        input_file = os.path.join(self.test_data_directory, 'fusions', 'MHC_Class_I', 'Test.all_epitopes.tsv')
+        output_file = tempfile.NamedTemporaryFile()
+        binding_filter.main([input_file, output_file.name])
+
+    def test_download_example_data_compiles(self):
+        compiled_run_path = py_compile.compile(os.path.join(
+            self.pVac_directory,
+            "tools",
+            "pvacfuse",
+            "download_example_data.py"
+        ))
+        self.assertTrue(compiled_run_path)
+
+    def test_download_example_data_runs(self):
+        output_dir = tempfile.TemporaryDirectory()
+        download_example_data.main([output_dir.name])
+
+    def test_top_score_filter_compiles(self):
+        compiled_run_path = py_compile.compile(os.path.join(
+            self.pVac_directory,
+            "tools",
+            "pvacfuse",
+            "top_score_filter.py"
+        ))
+        self.assertTrue(compiled_run_path)
+
+    def test_top_score_filter_runs(self):
+        input_file = os.path.join(self.test_data_directory, 'fusions', 'MHC_Class_I', 'Test.all_epitopes.tsv')
+        output_file = tempfile.NamedTemporaryFile()
+        top_score_filter.main([input_file, output_file.name])
+
+    def test_valid_alleles_compiles(self):
+        compiled_run_path = py_compile.compile(os.path.join(
+            self.pVac_directory,
+            "tools",
+            "pvacfuse",
+            "valid_alleles.py"
+        ))
+        self.assertTrue(compiled_run_path)
+
+    def test_valid_alleles_runs(self):
+        valid_alleles.main(["-p", "SMM"])
+
     def test_pvacfuse_pipeline(self):
         with patch('requests.post', unittest.mock.Mock(side_effect = lambda url, data, files=None: make_response(
             data,