DI-809 refactor

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+omit = tests/*

.github/workflows/pytest.yml

@@ -0,0 +1,28 @@
+name: pytest
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.8
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pipenv codecov pytest pytest-cov pytest-mock pytest-subtests
+        pip install -r requirements.txt
+        pipenv install --dev
+    - name: Install bedtools
+      run: |
+        wget https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static -O bedtools
+        chmod a+x bedtools
+        sudo mv bedtools /usr/bin/bedtools
+
+        bedtools
+    - name: Test with pytest
+      run: |
+        pytest -vv --cov .

.gitignore

@@ -0,0 +1,4 @@
+*.vcf*
+*.bed
+*.pyc
+.coverage

README.md

@@ -1,8 +1,8 @@
 <!-- dx-header -->
-# dnanexus_vcf_QC (DNAnexus Platform App)
+# eggd_vcf_qc (DNAnexus Platform App)
 
 ## What does this app do?
-This app runs a python script to perform simple vcf QC.
+This app runs a python script to calculate the mean het, mean hom and het:hom ratio of non reference variants in a given vcf.
 
 ## What are typical use cases for this app?
 This app should be executed stand-alone or as part of a DNAnexus workflow for a single sample.
@@ -11,20 +11,14 @@ This app should be executed stand-alone or as part of a DNAnexus workflow for a
 The app requires a VCF file (.vcf) containing variants to be evaluated and a bed file defining the regions within which variants in the vcf should be evaluated.
 
 ## What does this app output?
-The app outputs one file, where [outPrefix] is the vcf filename without extension:
-1. [outPrefix].vcf.QC is a tab delimited file containing:
- - sample id
- - mean het ratio (mean AAF of het variants)
- - mean homo ratio (mean AAF of hom variants)
- - het:homo ratio (ratio of het to hom variants on autosomes)
- - X homo:het ratio (ratio of het to hom variants on chrX)
- - gender (inferred from X homo:het ratio)
-
-## How does this app work?
-The app runs a bash script which runs the python script which generated the output file. The output file is then uploaded to dnanexus.
-
-## What are the limitations of this app
-- Inferred gender is tuned to work with TSOE data and the TSOnePlus.bed. Use of other assays/bed files may result in incorrect inferred gender.
-- Inferred gender may generate incorrect results for biological reasons e.g. for patient's whose parents are closely related, or patients with sex chromosome anomolies (Turner, Klinefelter etc.)
+The app outputs one tab delimited file `[vcf_prefix].vcf.qc`, where `vcf_prefix` is the vcf filename without extension:
+
+* sample id
+* mean het ratio (mean AAF of het variants)
+* mean hom ratio (mean AAF of hom variants)
+* het:hom ratio (ratio of het to hom variants on autosomes)
+* X het:hom ratio (ratio of het to hom variants on chrX)
+
 
 ## This app was made by EMEE GLH
+

dxapp.json

@@ -1,12 +1,10 @@
 {
-  "name": "eggd_vcf_qc_v1.0.1",
-  "title": "eggd_vcf_qc_v1.0.1",
+  "name": "eggd_vcf_qc",
+  "title": "eggd_vcf_qc",
   "summary": "Simple QC of a vcf file. Includes deviation from expected allelic balance",
   "tags":["NGS QC"],
-  "properties": {
-    "githubRelease": "v1.0.1"
-  },
   "dxapi": "1.0.0",
+  "version": "2.0.0",
   "inputSpec": [
     {
       "name": "vcf_file",
@@ -22,7 +20,6 @@
       "help": "A bed file containing the regions to be evaluated in the vcf file",
       "class": "file",
       "optional": false,
-      "default":{"$dnanexus_link":{"project":"project-Fkb6Gkj433GVVvj73J7x8KbV", "id":"file-FkyGjY8433GXG33JF06B9pKP"}},
       "patterns": ["*.bed"]
     }
   ],
@@ -33,7 +30,7 @@
       "patterns": [
         "*"
       ],
-      "help": "A tab delimited vcf.QC file"
+      "help": "A tab delimited vcf.qc file"
     }
   ],
   "runSpec": {
@@ -42,23 +39,30 @@
         "hours": 1
       }
     },
-    "execDepends": [
-      {"name": "pysam",
-       "package_manager": "pip",
-       "version": "0.12.0"}
-     ],
-    "interpreter": "bash",
-    "release": "16.04",
+    "interpreter": "python3",
+    "release": "20.04",
+    "version": "0",
     "distribution": "Ubuntu",
-    "file": "src/dnanexus_vcf_QC.sh"
+    "file": "src/vcf_qc.py",
+    "assetDepends": [
+      {
+        "name": "bedtools",
+        "project": "project-Fkb6Gkj433GVVvj73J7x8KbV",
+        "folder": "/app_assets/bedtools/bedtools_v2.30.0/",
+        "version": "2.30.0"
+      }
+    ]
   },
   "access": {
     "project": "CONTRIBUTE",
-    "allProjects": "VIEW",
-    "network": [
-      "*"
-    ]
+    "allProjects": "VIEW"
   },
+  "developers":[
+      "org-emee_1"
+  ],
+  "authorizedUsers": [
+      "org-emee_1"
+  ],
   "regionalOptions": {
     "aws:eu-central-1": {
       "systemRequirements": {

requirements.txt

@@ -0,0 +1,2 @@
+dxpy==0.382.0
+pysam==0.18.0