From bcd472baff09b5a997bcd48f89669d4c39bfd08d Mon Sep 17 00:00:00 2001
From: TheRiPtide <g.zaugg97@gmail.com>
Date: Wed, 15 Dec 2021 11:17:58 +0100
Subject: [PATCH] patch: cli for poly(A) classifier and coverage exclusions
---
setup.cfg | 10 ++++++-
src/polyA_classifier/__init__.py | 1 +
src/polyA_classifier/cli.py | 30 +++++++++++++++++++
.../polyA_classifier.py | 0
tests/test_poly_a.py | 2 +-
5 files changed, 41 insertions(+), 2 deletions(-)
create mode 100644 src/polyA_classifier/__init__.py
create mode 100644 src/polyA_classifier/cli.py
rename src/{ => polyA_classifier}/polyA_classifier.py (100%)
diff --git a/setup.cfg b/setup.cfg
index 1d48b94..4ae1933 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,3 +1,11 @@
[flake8]
max-line-length = 120
-docstring-convention = google
\ No newline at end of file
+docstring-convention = google
+
+[coverage:report]
+exclude_lines =
+ if __name__ == '__main__':
+
+[coverage:run]
+omit =
+ */cli.py
\ No newline at end of file
diff --git a/src/polyA_classifier/__init__.py b/src/polyA_classifier/__init__.py
new file mode 100644
index 0000000..0f5ce03
--- /dev/null
+++ b/src/polyA_classifier/__init__.py
@@ -0,0 +1 @@
+"""Module for classifying poly(A) sequences."""
diff --git a/src/polyA_classifier/cli.py b/src/polyA_classifier/cli.py
new file mode 100644
index 0000000..397ccf8
--- /dev/null
+++ b/src/polyA_classifier/cli.py
@@ -0,0 +1,30 @@
+"""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))
diff --git a/src/polyA_classifier.py b/src/polyA_classifier/polyA_classifier.py
similarity index 100%
rename from src/polyA_classifier.py
rename to src/polyA_classifier/polyA_classifier.py
diff --git a/tests/test_poly_a.py b/tests/test_poly_a.py
index 1f3760c..8c95e90 100644
--- a/tests/test_poly_a.py
+++ b/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
--
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