Add automated tests, add Binder link

.github/workflows/build-test.yml

@@ -0,0 +1,32 @@
+name: Build & Test
+
+on:
+  push:
+  schedule:
+  - cron:  '0 3 * * 1'
+
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update -f environment.yml
+        pip install . --no-deps
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest test

README.md

@@ -2,6 +2,8 @@
 
 Convenience Python APIs for antibody numbering using [ANARCI](https://github.com/oxpig/ANARCI)
 
+Try it out in your browser using Binder: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/prihoda/AbNumber/HEAD?filepath=examples%2FAbNumber_getting_started.ipynb)
+
 ## Installation
 
 Install using Bioconda:

abnumber/germlines.py

@@ -31,7 +31,7 @@ def get_imgt_chain(gene_name):
 
 def get_imgt_v_chains(chain_type=None):
     global _HUMAN_IMGT_V_CHAINS
-    if _HUMAN_IMGT_V_CHAINS is None:
+    if _HUMAN_IMGT_V_CHAINS is None or chain_type not in _HUMAN_IMGT_V_CHAINS:
         _HUMAN_IMGT_V_CHAINS = {}
         for t, germlines in HUMAN_IMGT_IG_V.items():
             positions = germlines['positions']
@@ -42,7 +42,7 @@ def get_imgt_v_chains(chain_type=None):
 
 def get_imgt_j_chains(chain_type=None):
     global _HUMAN_IMGT_J_CHAINS
-    if _HUMAN_IMGT_J_CHAINS is None:
+    if _HUMAN_IMGT_J_CHAINS is None or chain_type not in _HUMAN_IMGT_J_CHAINS:
         _HUMAN_IMGT_J_CHAINS = {}
         for t, germlines in HUMAN_IMGT_IG_J.items():
             positions = germlines['positions']

environment.yml

@@ -0,0 +1,11 @@
+channels:
+  - nodefaults
+  - bioconda
+  - conda-forge
+dependencies:
+  # Dependencies for local setup only. Make sure to update meta.yml in bioconda channel.
+  - python >= 3.6
+  - pip
+  - pandas
+  - biopython
+  - anarci == 2020.04.23

examples/AbNumber_getting_started.ipynb

@@ -7,6 +7,15 @@
     "# AbNumber Usage Examples"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!conda install -y -c bioconda abnumber"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

test/test_bugs.py

@@ -0,0 +1,35 @@
+import pytest
+from abnumber import Chain, ChainParseError, Position
+from abnumber.germlines import HUMAN_IMGT_IG_V, HUMAN_IMGT_IG_J
+
+
+def test_imgt_61A():
+    """Related to ANARCI issue: https://github.com/oxpig/ANARCI/issues/14"""
+    assert Position.from_string('61A', 'H', 'imgt') > Position.from_string('61', 'H', 'imgt')
+    seq = 'EVQLVESGGGLVQPGGSLRLSCAASGIILDYYPIGWFRQAPGKEREGVAFITNSDDSTIYTNYADSVKGRFTISRDKNSLYLQMNSLRAEDTAVYYCSSKASFLIGKDDQGIDAGEYDYWGQGTMVTVSS'
+    with pytest.raises(NotImplementedError):
+        chain = Chain(seq, 'imgt')
+
+
+def test_light_chain_IMGT_position_21():
+    # Check bug from ANARCI 2021.02.04
+    # When numbering full Kappa chains, position IMGT 21 contains a gap
+    # When numbering V gene only, position IMGT 21 contains an amino acid as expected
+    # Test against this by making sure that same numbering is assigned when numbering V gene and VJ genes concatenated
+    # https://github.com/oxpig/ANARCI/issues/17
+    for germline in HUMAN_IMGT_IG_V['K']['aligned_sequences']:
+        v_seq = HUMAN_IMGT_IG_V['K']['aligned_sequences'][germline].replace('-', '')
+        first_j_gene = list(HUMAN_IMGT_IG_J['K']['aligned_sequences'].keys())[0]
+        j_seq = HUMAN_IMGT_IG_J['K']['aligned_sequences'][first_j_gene].replace('-', '')
+        vj_seq = v_seq + j_seq
+        try:
+            v_chain = Chain(v_seq, 'imgt')
+            vj_chain = Chain(vj_seq, 'imgt')
+        except Exception as e:
+            print(e)
+            continue
+        v_positions = [str(p) for p in v_chain.positions]
+        vj_positions = [str(p) for p in vj_chain.positions]
+
+        len_limit = len(v_seq) - 20
+        assert ','.join(v_positions[:len_limit]) == ','.join(vj_positions[:len_limit])

test/test_chain.py

@@ -214,14 +214,6 @@ def test_multiple_domains():
         chain = Chain(vh + vl, 'imgt')
 
 
-def test_imgt_61A():
-    """Related to ANARCI issue: https://github.com/oxpig/ANARCI/issues/14"""
-    assert Position.from_string('61A', 'H', 'imgt') > Position.from_string('61', 'H', 'imgt')
-    seq = 'EVQLVESGGGLVQPGGSLRLSCAASGIILDYYPIGWFRQAPGKEREGVAFITNSDDSTIYTNYADSVKGRFTISRDKNSLYLQMNSLRAEDTAVYYCSSKASFLIGKDDQGIDAGEYDYWGQGTMVTVSS'
-    with pytest.raises(NotImplementedError):
-        chain = Chain(seq, 'imgt')
-
-
 def test_germline_assignment():
     light_seq = 'ELVMTQSPSSLSASVGDRVNIACRASQGISSALAWYQQKPGKAPRLLIYDASNLESGVPSRFSGSGSGTDFTLTISSLQPEDFAIYYCQQFNSYPLTFGGGTKVEIK'
     light_chain = Chain(light_seq, scheme='imgt', assign_germline=True)