Merge pull request #12 from ratschlab/development

Prepare release

.circleci/config.yml

@@ -0,0 +1,23 @@
+version: 2
+jobs:
+  build:
+    docker:
+      - image: circleci/python:2.7.15-stretch-node
+    steps:
+      - checkout
+      - run:
+          name: setup environment
+          command: |
+            mkdir ~/env
+            virtualenv ~/env
+            source ~/env/bin/activate
+            pip install -r requirements_dev.txt
+            pip install -r requirements.txt
+      - run:
+          name: running tests
+          command: |
+            mkdir ~/test_reports
+            source ~/env/bin/activate
+            pytest --junitxml=~/test_reports/pytest-results.xml
+      - store_test_results:
+          path: ~/test_reports

.gitignore

@@ -45,6 +45,7 @@ nosetests.xml
 coverage.xml
 *.cover
 .hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo
@@ -102,3 +103,7 @@ ENV/
 
 # Pycharm
 .idea
+
+# intermediate test data
+tests/data/genome/
+/scripts/generate_gt_file.py

immunopepper/__init__.py

@@ -0,0 +1,5 @@
+"""Top-level package for ratschlab common."""
+
+__author__ = """Ratschlab"""
+__email__ = '[email protected]'
+__version__ = '1.0.0'

immunopepper/constant.py

@@ -0,0 +1,13 @@
+'''
+In some cases, the output does not exist. So a special character is used in the output file.
+Mainly on the flag field and expression counts field in the output .tsv file
+For example,
+
+- flag field IS_IN_JUNCTION_LIST if no external junction file is provided
+- flag field JUNCTION_ANNOTATED if it is an isolated exon
+- field VARIANT_COMBINE if no variant existing in the exon-pair
+- expression field VARIANT_SEG_EXPR if no variant existing in the exon-pair
+- expression field JUNCTION_EXPR if it is an isolated exon
+'''
+
+NOT_EXIST = '.'