patch: cli for poly(A) classifier and coverage exclusions

setup.cfg

 [flake8]
 max-line-length = 120
-docstring-convention = google
+docstring-convention = google
\ No newline at end of file
+
+[coverage:report]
+exclude_lines =
+    if __name__ == '__main__':
+
+[coverage:run]
+omit =
+    */cli.py
\ No newline at end of file

src/polyA_classifier/__init__.py

+"""Module for classifying poly(A) sequences."""

src/polyA_classifier/cli.py

+"""Command-line interface for the poly(A) classifier."""
+
+import sys
+import argparse
+from src.polyA_classifier.polyA_classifier import PolyAClassifier
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('data', action='store', help='str or list(str) of length 200 chars to classify.')
+parser.add_argument('-p', '--path', action='store', help='Path to state-dict for Net-model.',
+                    default='./models/internal_priming.pth')
+
+
+if __name__ == '__main__':
+
+    args = parser.parse_args()
+
+    if args.data[0] == '[':
+
+        data = args.data[1:-1].replace(' ', '').split(',')
+
+    else:
+
+        data = args.data
+
+    classifier = PolyAClassifier(state_dict_path=args.path)
+
+    result = classifier.classify(data)
+
+    sys.stdout.write(str(result))

tests/test_poly_a.py

@@ -3,7 +3,7 @@
 import pytest
 import os
 from src.poly_a import generate_poly_a
-from src.polyA_classifier import PolyAClassifier, Net
+from src.polyA_classifier.polyA_classifier import PolyAClassifier, Net
 import linecache