Merge pull request #21 from ave-dcd/Transcripts

Transcripts

.github/workflows/python-package.yml

@@ -0,0 +1,35 @@
+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+    env:
+        PATH_TO_SEQREPO: ./tests/data/seqrepo/latest
+        HG38_FILE: ./tests/data/hg38.2bit
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      - name: Test with pytest
+        env:
+          PATH_TO_SEQREPO: ./tests/data/seqrepo/latest
+          HG38_FILE: ./tests/data/hg38.2bit
+          GENE_NORM_DB_URL: postgres://postgres@localhost:5432/gene_normalizer
+
+        run: |
+          export PYTHONPATH="${PYTHONPATH}:$(pwd)"
+          pytest

mavedb_mapping/__init__.py

@@ -1,13 +1,17 @@
+
 import os
-from gene.query import QueryHandler
-from gene.database import create_db
 from biocommons.seqrepo import SeqRepo
-from ga4gh.vrs.dataproxy import SeqRepoDataProxy
+
 from cool_seq_tool.data_sources.uta_database import UTADatabase
 
+from ga4gh.vrs.dataproxy import SeqRepoDataProxy
+
+from gene.query import QueryHandler
+from gene.database import create_db
+
 path_to_seqrepo = os.getenv("PATH_TO_SEQREPO", "/usr/local/share/seqrepo/latest")
 path_to_hg38_file = os.getenv("HG38_FILE", "hg38.2bit")  # default- in current directory
-data_file_path = "mavedb_mapping/tests/data/"
+data_file_path = "tests/data/"
 
 # utadb = UTADatabase(db_pwd="uta")
 qh = QueryHandler(create_db())