{"action":"created","comment":{"url":"https://api.github.com/repos/VirologyCharite/Daniela-mutation-frequency/pulls/comments/231508258","pull_request_review_id":172493607,"id":231508258,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIzMTUwODI1OA==","diff_hunk":"@@ -0,0 +1,157 @@\n+#!/usr/bin/env python3\n+\n+from unittest import TestCase\n+from dark.reads import Read, Reads\n+from collections import Counter, defaultdict\n+from heterogeneous_sequences import heterogeneousSites, compareToRef\n+\n+\n+class TestHeterogeneousSites(TestCase):\n+    \"\"\"\n+    Test the heterogeneousSites function.\n+    \"\"\"\n+\n+    def testOneRead(self):\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read])\n+\n+        self.assertEqual({}, heterogeneousSites(reads, len(read), 1))\n+\n+    def testHomogeneousReads(self):\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read, Read('id2', 'ACCG')])\n+\n+        self.assertEqual({}, heterogeneousSites(reads, len(read), 1))\n+\n+    def testHeterogeneousReadsOneDifference(self):\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read, Read('id2', 'ACCC')])\n+\n+        self.assertEqual({3: Counter({'G': 1, 'C': 1})}, heterogeneousSites(reads, len(read), 1))\n+\n+    def testHeterogeneousReadsTwoDifferences(self):\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read, Read('id2', 'TCCC')])\n+\n+        self.assertEqual({0: Counter({'A': 1, 'T': 1}), 3: Counter({'G': 1, 'C': 1})}, heterogeneousSites(reads, len(read), 1))\n+\n+    def testHeterogeneousReadsFractionHigh(self):\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read, Read('id2', 'ACCC'), Read('id3', 'ACCC')])\n+\n+        self.assertEqual({3: Counter({'G': 1, 'C': 2})}, heterogeneousSites(reads, len(read), 0.7))\n+\n+    def testHeterogeneousReadsFractionLow(self):\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read, Read('id2', 'ACCC'), Read('id3', 'ACCC')])\n+\n+        self.assertEqual({}, heterogeneousSites(reads, len(read), 0.6))\n+\n+    def testHeterogeneousReadsFractionLowWithOneDifference(self):\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read, Read('id2', 'TCCG'), Read('id3', 'TCCG'), Read('id4', 'ACCG')])\n+\n+        self.assertEqual({0: Counter({'A': 2, 'T': 2})}, heterogeneousSites(reads, len(read), 0.6))\n+\n+    def testGaps(self):\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read, Read('id2', '-CC-')])\n+\n+        self.assertEqual({}, heterogeneousSites(reads, len(read), 1))\n+\n+    def testEmptyReads(self):\n+        reads = Reads()\n+\n+        with self.assertRaisesRegex(NameError, ''):\n+            heterogeneousSites(reads, len(read), 1)\n+\n+class TestCompareToReference(TestCase):\n+    \"\"\"\n+    Test the compareToRef function.\n+    \"\"\"\n+\n+    def testEmtpyReference(self):\n+        referenceread = Read('', '')\n+\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read])\n+\n+        with self.assertRaisesRegex(ValueError, 'Reference read length is not the same as length of other reads.'):\n+            compareToRef(referenceread, reads, len(read))\n+\n+    def testNoRead(self):\n+        referenceread = Read('idref', 'ACCG')\n+\n+        reads = Reads()\n+\n+        self.assertEqual({}, compareToRef(referenceread, reads, len(referenceread)))\n+\n+    def testOneReadNoDifference(self):\n+        referenceread = Read('idref', 'ACCG')\n+\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read])\n+\n+        self.assertEqual({}, compareToRef(referenceread, reads, len(read)))\n+\n+    def testOneReadOneDifference(self): \n+        referenceread = Read('idref', 'ACCG')\n+\n+        read = Read('id', 'ACCA')\n+        reads = Reads([read])\n+\n+        self.assertEqual({'G to A': 1}, compareToRef(referenceread, reads, len(read)))\n+\n+    def testAllPossibleDifferences(self):\n+        referenceread = Read('idref', 'AAACCCGGGTTT')\n+\n+        read = Read('id', 'CGTAGTACTACG')\n+        reads = Reads([read])\n+\n+        self.assertEqual({'A to C': 1, 'A to G': 1, 'A to T': 1, 'C to A': 1, 'C to G': 1, \n+            'C to T': 1, 'G to A': 1, 'G to C': 1, 'G to T': 1,'T to A': 1, 'T to C': 1, \n+            'T to G': 1}, compareToRef(referenceread, reads, len(read)))\n+\n+    def testTwoReadsTenDifferences(self): \n+        referenceread = Read('idref', 'ACCGGG')\n+\n+        read = Read('id', 'AGGAAA')\n+        reads = Reads([read, Read('id2', 'AGGAAA')])\n+\n+        self.assertEqual({'C to G': 4, 'G to A': 6}, compareToRef(referenceread, reads, len(read)))\n+\n+    def testGapInReference(self):\n+        referenceread = Read('idref', 'ACC-')\n+\n+        read = Read('id', 'ACCG')\n+        reads = Reads([read])\n+\n+        self.assertEqual({}, compareToRef(referenceread, reads, len(read)))\n+\n+    def testGapInReadNoMutation(self):","path":"test_heterogeneous_sequences.py","position":131,"original_position":131,"commit_id":"62b57c5d0cb6094204de1fa38e77e74c17761920","original_commit_id":"62b57c5d0cb6094204de1fa38e77e74c17761920","user":{"login":"terrycojones","id":132978,"node_id":"MDQ6VXNlcjEzMjk3OA==","avatar_url":"https://avatars3.githubusercontent.com/u/132978?v=4","gravatar_id":"","url":"https://api.github.com/users/terrycojones","html_url":"https://github.com/terrycojones","followers_url":"https://api.github.com/users/terrycojones/followers","following_url":"https://api.github.com/users/terrycojones/following{/other_user}","gists_url":"https://api.github.com/users/terrycojones/gists{/gist_id}","starred_url":"https://api.github.com/users/terrycojones/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/terrycojones/subscriptions","organizations_url":"https://api.github.com/users/terrycojones/orgs","repos_url":"https://api.github.com/users/terrycojones/repos","events_url":"https://api.github.com/users/terrycojones/events{/privacy}","received_events_url":"https://api.github.com/users/terrycojones/received_events","type":"User","site_admin":false},"body":"Your tests should have docstrings that explain what they're trying to test. Else you're mking every reader try to figure it out for themselves, and the reader can't judge whether your code is right because they don't know what it's trying to 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