Add tests for parsemarkers

test/data/marker.fna

@@ -0,0 +1,2 @@
+>abc
+GTGGTGAGTGCTTGGACGTGTGTGGTGATGCTCATGGTGTCTTCCCCCCTTCCCCGTGTTGTTACCACCCACTCTACCCGCTCACACTTTCGAATACAAGGGTATTTTTCGAAATGGAAAAGCTGTCGAGCACTCACATGTTCGACAGCTTCATATGTCCTTGAACTACGTAACTTTTTCCTTACAATCAGCGCAAAGTCCAAAGATTTCGGCCTCGTGACTACTGAGAGCAAAGCCGTTTTTAGTGGCAATTTCCTGTGCCCATGTCTCTACTGGACCGCCATCGATTTCGACTGTGTGACCGCAATTGGTGCAGACCAAGTGATGGTGGTGTCCCTCGTCGTGGCATTGGCGGTACAGAGTTTCTCCACCTGTGACGGTAAGTACGTCGACTGCCCTGATGTCCGCGAGGGATTGGAGGGTTCGGTAGACGGTTGTGAGGCCGACGTTGTGTTCCCTGGTGGATAGCTCGTGATGGATTTCTTTGGCGGAAGCGAAGTTATCGATTTCCTCAAGAACGTCAATTACGGCTTTTCGCTGTCTGGTGCTTCGCACTCCCAGCTTCGGGGCAGAGCCTTGGCTGATGCGATTGATACCCACCGTTGATCCTCCTCAATGACACAAAATGTACTTCGATAGTCTACCCAGATGTGTCAACCCCTGCGTTTAGTGCCAGGAGAAGTATGTCGAGGACGAGTGGTTCGGCAAGTGAATAAGTCATTTGCCGGCCTTGACGTTCTGCGTCGACGATACCTGCAGTTTTAAGGACTTTGAGGTGTTGGCTCACTAGTGGTTGCGAACTTTTTACTAGCTTGACCAATTCGTGGACGTAGTGGGGCCTTTCGTTGAGGGCGAGGATGATTTCGATTCTTAAGGGGGAATCTAGTGCCCTAATCAGCAGGCTGATCGCTTTGATGTTTTTTGCTGTTGCAAGTTTCTGAAGCTCAGCTGATGCTGTGGATTCGGACTCTTCTGCAGGGGTGACGAAATTCCGATTTGAGTGTTGAGCCACGGGGAAGTCCTTCCGTCCTTAGGCTAGGTCTGGAATGGATCTAGCACGCTTGCTATTTTACCTTCTATATAAACCTTTTATGAGGGAAATGAAAAAATAGTTATTAGAACTAGTTTACATCGCGAAGGCCGCAAAATGACGGGGTCAGCGGAAGCAACATCGTTAGTTGGGCTAGGATTGGTTGGGTATGTCCTAAAAGGGACGGTTATTTTTTCATTCGACGTGGAGGAGAGCATCCGACGTGGCTCAGCAATCGATCATCGACACCGTGGTTAACCTGTGTAAACGACGTGGACTGGTGTACCCCTGTGGTGAGATCTACGGCGGTACCCGCTCTGCGTGGGACTACGGCCCGCTGGGTGTGGAGCTGAAGGAAAACATCAAGCGCCAGTGGTGGCGTTCTATGGTTACTTCCCGCCCAGATGTTGTGGGTGTTGATACTTCTGTCATCCTTCCTCGCCAGGTGTGGGTAACTTCCGGCCACGTTGAGGTCTTCACTGACCCACTGGTTGAGTCTTTGAACACCCACAAGCGTTACCGTGCGGACCACCTGCTGGAGCAGTACGAAGAGAAGCATGGTCACCCACCTGTAAACGGCTTGGCTGACATCAACGATCCAGAGACCGGCCAGCCAGGTAACTGGACTGAGCCTAAGGCGTTCTCTGGTCTTCTGAAGACTTTCTTGGGACCTGTGGACGACGAAGAGGGTCTGCACTACCTGCGCCCTGAAACTGCTCAGGGTATCTTCGTGAACTTCAAGAACGTGATGAACACTTCACGCATGAAGCCACCTTTCGGTATCGCGAACATCGGTAAGTCTTTCCGTAACGAGATCACCCCAGGTAACTTCATTTTCCGTACTCGTGAGTTCGAGCAGATGGAGATGGAGTTCTTCGTCAAGCCTGGTGAGGACGAAGAGTGGCACCAGCACTGGATTGATACTCGCCTGCAGTGGTACATCAACCTGGGCATTAAGCCTGAGAACCTGCGTCTGTACGAGCACCCTCAGGAGAAGCTGTCTCACTACTCCAAGCGCACTGTTGATATTGAGTACGCATTCAACTTTGCTAACACCAAGTGGGGCGAGTTAGAGGGTATCGCGAACCGTACTGATTACGATCTTCGCGTGCACTCTGAGGGCTCTGGTGAGGACCTGTCATTCTTCGATCAGGAGACCAATGAGCGTTGGATTCCTTTCGTAATCGAGCCTGCTGCAGGTCTTGGTCGCGCAATGATGATGTTCCTGATGGATGCTTATCACGAGGACGAGGCACCAAACTCAAAGGGTGGCGTCGATAAGCGTGTTGTTCTGAAGCTTGACCGTCGCCTTGCGCCGGTTAAGGTTGCGGTCTTGCCGCTGTCAAAGAAGGACACTTTGACGCCTTTGGCGGAAAAGCTCGCAGCAGAGCTGCGTGAATTCTGGAACGTTGATTACGACACTTCAGGTGCGATTGGTCGCCGTTACCGTCGTCAGGACGAGATCGGTACTCCATTCTGCGTCACCGTTGACTTTGATTCTCTCGAGGACAACGCTGTGACCGTGCGTGAGCGCGACACCATGGAGCAGGTTCGTGTTCCACTTGATGAGCTGCAGGGTTACTTGGCTCAGCGCCTCATCGGCTGCTAAACGGCAACCAATAGAGCGATAATTCGCTAAGACGAATGTAATCGCAGCAACATATAGCACCGGCTTAACAGGCCGGTGCTATTCTGTTCGCATGACTTCGAAGGATCTGATTGTGACCTCCTATACGTCTTGGGGCAAGCGTTTCAAGAATGACGGGAAGCTTTTTATTAACCTACTTCGCAGCACCACTGATAGTGCTGATGAAAAGGTTTTAGCCACTTTCGGTGAAGTTCCCAGCAAATCATTTGAAACCACCGCAACGGTTGATGAGCAGCAGTGGGAACTGTCCTTCAATATTGATGGAACGGCAACTGCCAAGCTTCCTGATGGTCGTGTGTTCAGCGCGAATGCAGGTGAGAAGACCTTTACCAAGTCCAAGCGGATTGAAATCGACATGGACGGCACCGCGATGGCTGCTGTTAATGAAGATAAAAACAATTGGATTATCGACGATTCTGAAGAGAATAAAGTCGCTCAGTTTACCGGTATGAACAACGGTGTGCGTCGCGCGATTGTGGAGTTTGAGCCTGACGTAGAAGTCACCCAGGAGCAGGAAATTTTCTTGTCGTGGGTTGCTCGGAAAACTCTGGAATCCCGCATGTTGGGCTCCAGTTGGGGACTGACTCTGTTTTTGATCATTTTGACGCCAATCATTATTTTTCTCACTTTCAGCTAAAAGGACCATGCAATGGTAGACGCTCAGCGCCCCAAAGCAGGCATCTTCGGTAGCCACACAGAAGAAACATGGGTGTGGCTCGGTAATGAACTTTTCGACGAGTCCGGCGAGGTCATCGCCGACGTTCGCTCCGACGTCCTCTACGTGGATCGCGAACGACTACTCATCGAATCCACCCCCGGCACCATGCGTTTTCGTTGCCGCGCAACACTGTCCGGGGGTGAGGTCTATACAATGACTCAGAATTCTTTCACTGTGGGGGATCTCACTGCGGTGTGCGGGCGCCGGACGTATTCGCTAAAAAGGGTGTCGCCGTGGCGTAAAGAACGCCTGATCACCAACAATGGGGTGGAAGTGGCGCGACTTCGCCCGATGACCAGCGGTAAAGTCGAATTCATTGTGGGCACCGCGGACAGCGAGGCGTTGCCGTTCGTCGACGCAGTATTTTTGAGCTGGGCGTGCGTCCTGGTGGATTCGGCCGTGCGCCGGCCGAAAATTTAAAAGCTTTTTGCTTATCGACGCACCCCTCCACCTGTTTTTTGTAGCCGGGGGATCATTTCCTTTGAAGGATCCAATCTCCGCACTTAGTTTCCTTCGGTGTGAAGGAAAGAGTTCCGTAAAGACCTCTATCTCATTTAAAGAAGTGGAGGATTAGGGTCGTTGACTCGCCTTCGGCACTAATTTGAGCCAAGTTCAAGTTTGCTGCCATCCCAGGTGACCGAAAATGTCCTATGCGAGGTCTCTTCGGTCACTTGGTTTTGCTCGTTTCAGGCTAGAAGCGGCCTCCGCGGAACCCTCCTCCGCCACCGCCACCACCGCTGAAGCCGCCACCGCCTCCACCGAAGCCTCCACCGAAACCGCCACCGCGGCCGCTGTTGAGAATCGAGTTGATCACCATGCCGGTGACAATCGCACCGGTGGTTCCGCCACCGGAATTGTGGCGATTGTTGTAGGTGGTGATGTCGTTTTGTGCTGACTTGCTGGCGCGTTGGGCTGCGACTGCTGCTTGACGTCCGTAATCAATTCCTGCACGGGTGTCGCGGGTGCGGTTTTGTTGTGCCATGGCGTACAGTTTTTGTGCGTTGGCCAGGTGGGTGCGGGCTTCGGATTTTACGATGCGACCGCGGGTGGAGATGAGGTCTTCGGCCTTTTGGATTTGGCTTCTTGCAGATTGCAGCTGTTGGTCGAATACGCGTAGCTGGCGGGCTTGATCAGCTGCGGTGGCGCGAAGTGTGTCAAGTTGAGTGTCGAGGGCGGAGTCGACATCGACAAGTTCTGTGTAGGTTCCGAGCGGATCCTTTTCGGCGTCTGCTGATGCGGTGGTTAGTGCTGCGCTGGCTGCGCGGACAGCATCGTCGAGGGAGGCCCAGTCGGCACGGGCACCGTCGGCTCCTGCGCTTTGTTTGAGTTGGCCGGCTTCGTTGATTTCGTCTGAGATTTCTTGAATCAGATCGGCAACGTTTGCTTTGGCTGTGGAGATGTTTTCATCGGCATGCTCGACGCCCTCGAGGAGTTTGTCTGCGGTAGTGATGGCGTGCTCGATGTGACGGATCGCGTCGATAAGCCCGCCCTGCTCGCCTGCGGGCATGGACTCTATCTTGTACGCCTGTGGCAGGACTTCTTCTGCTTCGTCGAGCGAAGCGCTGGCGAGGTCGACGTTGTCGTCGATGCTTTCAAGGACCTCTGCTGAGTAGCGAGCGCGCAGGCCAGCGAGTGTTTCTTGAGCCTTGGGGAGGCGGGTGCGCAGGTCGACGGATTTTTGGGTGAGAGCATCCAATTTGCTGCCCGCGTTGATCAGCAGGTTGCGCATATCGGCAAAGTTTTGGGCCTCGGCGTCGAGGGCATCGTCGGCTTGGCCACAGGATGAAATGATTTCTACCAGCATGGATCGACGTTCGGCTTCGGATTCTGGGATAGAATCGTTGAGGCGCTGCTGAATCTCAAAGGCTTTTTGCAGGGTGCCGGTGGAGTGGTTCATGGCGCGGTTGAAGCTGCGGGTGCGCTCTGGTCCGAACTCGGAGGTAGCGATAGCGAGCTCTTCTTTTCCGCGACGGATGGAGTCATCAGTGGAGGTGAGCTCTTCTTGGGCAAGGTGTTCGAGAGTTTCCATGGGAAGCTGCATGAGGCGGTTGGTATCGCGAGGGTCGATCTCACGTGCATCTTCCAAGGTTGCAGCACTTGTTTTCTTCTTGCGGCTGCGGGAATAGGCCCAAATTCCGCCACCAGCGGCCACTGTGCCAACGCCCGCAGCAGCCAACCAAGCGCCGGAAGATCCAGAAGAGCCTGAGGTTCCTGAGGCACCAGAACTAGAACCAACTGATTCTGCCAGCGCTAGTGCGGAGCCTGCCCAATCTTCTTGGGAAAGCGCCTGGAAAGCAGCGTTGTTGGCGGCGTCGAGTTCAGCGTCGGTCCATTGAGTACCACCTTGGATGCCGTACTGCCGTTCCTCGGGAGCGAGTGCATAAACCAAGACGTTTCCGCCGCCGTTGGCTTGGAGTGCTTGCTGCGTCCACGTTTCAGGGTCAACTCCGTCGAAAGAGCTTAGGAAAACAACGAAAATAACCTTTTGTTCAGATGCCTTTACATCATCGATGGCAGCCTGAATGTTGGTGATATCGGACGAGGAAATCTGGCCGGTGTAGTCAGTGACATTGTCTTGGTAAAATTCTGGTGATTCAGCCAAGACATATGTTTCTGTGGCTTCTGCAGTGTGAGCAGTAAAAAATGGTCCACTGATAAGGAGCGCGCCAGCTCCAATTGCCACAGTGACCGATACACGGCGGACGTTTTCCCGAAGATGCACCAAACTAAAGTTCATGGTCCCCACCTTAGACGAGTCCAGCTGGCACACTAGTTAACGTGAGAAGATTTTTAGCCAAGAGTTTACTCTTAACCGCAGTAGCGCAACCAGCCCTGAGGGTGGTCGCGTATTCGATGCTCAGAACGCCTAATAATCGGCACAAAATTGATTCAATTTTGGTGTTGGGCACAGCTCAATATGATGGGGTTCCATCGAGGCAGTTTGCTGCTCGTTTGAGGCATGCCGCGAAGCTGTGGCGTCTTCATGAAATCCAGCATGTATATACTGTCGGCGGAAAACTTCCTGGTGATCGTTTCACCGAAGCAGAAGTCGCGCGGGAGTATTTGATCAAAGAGGGCGTGGATCCGGATCTGATTTTTGTCTCTGCAGTTGGCAATGACACTGTCTCCTCCTATGAGGCGCTTGATCCGGAAAAGCTTGGTCGGGTGCTGATTGTTACTGATCCGAACCATTCGTATCGGGCGGTGCGCATCGCGCGACGCATGGGCTTTGACGCGAAACCTTCCCCGACAACCTATAGTCCCGCGAAGTTTCCGTCGATAGTTTATTTTCTGACCTTGTCCCATGAGTGGGGCGGGGTAGTGGTACAGGACGTGTCGTGGCTCTTGGGCGAACGGGTGGCCGATAAGGTGGAAGCATCTTTGCGAACTATCCAAGGCCTGCTGCGCCCTTCGAGGCGTGCGCGCCATGAGCAACTTCGGAGGCTGAAAAAGTAGATGTACCCCTATTCCGACGCAGACGCTTTTCGACGCCACCCTGAGCGCGCCAAGTCCAGCCAACTGCGCACCAGCGCCGTAGACACCCGCAGCGCGTTCGCCCGCGACCGGGCTCGCGTGCTGCATTCTGCTGCTCTTCGACGCCTCGCGGATAAAACCCAAGTGGTTGGCCCCAATGATGGTGATACTCCGCGCACCCGGCTGACGCACTCTTTGGAAGTAGCTCAAATTGCACGGGGAATCGGAGCTGGACTGGATTTGGATCCTGATCTGTGCGATCTGGCAGGGCTGTGCCATGACATTGGGCATCCGCCGTATGGACACAACGGTGAAAACGCGTTGAATGAAGTTGCTGCGGCCTGTGGAGGATTTGAGGGCAACGCCCAAACCTTGCGTATTCTCACGCGGCTGGAGCCAAAAATTGTCTCTGATGAGGGGGAGAGCTTTGGGCTGAACTTGTCGCGGGCTGCTCTTGATGCTGCATGTAAGTATCCGTGGGCTAAAACAAATGCGGATGGCAGTGTCAATAAGAAATACAGTGCTTATGATGAGGACGCAGAAATTCTTGCTTGGATCAGGCAAGGCCATGAAGACCTCAGACCACCAATCGAAGCTCAGGTCATGGACTTTTCCGATGATATTGCCTACTCAGTACACGATGTAGAAGACGGCATTGTTTCCGGTCGCATCGATTTGAAAGTGCTGTGGGACCTGGTGGAATTAGCAGCACTGGCGGACAAAGGCGCAGCAGCTTTCGGAGGCTCGCCTGCAGAACTCATCGAGGGCGCAGCCTCGTTGCGGGAGCTTCCTGTGGTAGCGGCCGCTGCAGATTTTGATTTCTCACTGCGTTCCTACGCTGCGCTGAAGGCCATGACCTCAGAACTAGTGGGAAGATACGTTGGCTCTACCATCGAGTCAACAAAGAAAACACACGCCGGCATTGATGTGGGACGCATGCACGGCGATTTGATCATTCCAGAAACAGCGGCCAGTGAAGTAAAACTGCTCAAAACGTTAGCGGTTCTCTATGTGATGGATGACCCAGGGCACCTTGCGCGCCAAAACAGGCAACGGGATCGTATCTTCCGGGTTTTTGACTACCTGGTGCTGGGGGCTCCGGGATCGTTGGATCCGATGTATCGCCAGTGGTTTATTGAAGCGGATTCAGAATCGGAACAGATCCGTGTGATTGTTGATCAGATTGCGTCGATGACGGAGTCTCGTCTGGAACGCCTTGCCCGGAATGCTGCTGACATCTCAGGATTCTTGGGATAGTTGGTTAGAGCAGCAGCGATTTTTAGTAAGGCCAATAACATGTTTTGGCTTAAACCTGTGTCGTGTCAGATGGTGGCGAAGTAGAGTTCGCAAAGCTAGCGAACATGAATTCGTGTTCAGGAACTTAACAGGGATCAAACAGAGAACAGAGAACAGATCACGCTGCCCAAAAATCGCACTTTTAAGGTTTGTGGGCGTCTGTGTGTGGTTTGCCGCTGTAAAGTATCACCACGTTATGCGCCCTGGTGTGATCAAGCGTTCGTTCTGGGTCGAAACCCCAAAAGTCACAATTCCCCAGAAGCGGGTCAAACCCATTTAGCTTATTGCTTACATATCGAGGGTTTAGAAAAGTGATTTGTCGGATCAGTCGGTTTCTGCCAAGTAAATAGAACTTTATAAATTTTGTGGCTCTCAAATCTTAGGCCACGGCTTCCGATTTGAACCGGAGGTTCAAAAGGCTTATATAGACAAGATTCTGCATCGTCTCACGAGCCCCTCATTGCCTGACACGGTCAATCGTGTGGGAGGTACCAATCCGTGAGATTTCTGCCAACGAGCGATTCATTGGCCCCGCTGCAGAGCTGGCAGAACACGGACATAACCCAAATAATCTGAGGTCTGCCGTTTGCAGCAGCATTAGCGTTTGATGTGGAAGGTGATGCAGAGGCTGTTGATCTGCAAGCGCGTCTTTCCCAAGCACGGGGGAACCCTGAAGCATCGGATGCTCTAGTTGCTGAGCTGACTGGTGTTACTGCTAATCATCCGTTGGTCAGTGCTTGTCTGAAGTTTCCGCTCAATCCTAAGCTTCTCAAGATTTCGTAAAAAAGCTGCCAACTACCGTAAAACCGCACTACTAGAGGAGTGCGTTTTTCGTTCCTGAACACATTGCGTGCTGCAACTTAATTATGGTCCTCCCAGCTCAGTGTGCTGTGTGGATTGTTTATTCTCGTCCATTAAGTGATCGAGAAAAAGTTGTTGTAAAGTCATGCGCATGTGTGGAATTGTTGGATATATTGGCCAGGCGGGCGACTCCCGTGATTACTTTGCGCTTGACGTCGTTTTAGAAGGACTGCGCCGACTTGAATACCGCGGTTATGATTCCGCAGGTGTAGCTGTTCATGCGAACGGTGAAATCAGCTACCGAAAGAAGGCTGGAAAGGTAGCTGCGCTGGACGCTGAGATCGCTCGCGCTCCTTTGGCGGATTCCATTTTGGCTATTGGTCACACCCGGTGGGCAACTCACGGTGGACCAACCGATGCAAATGCACACCCCCATGTTGTTGATGGCGGCAAGTTAGCTGTCGTACACAACGGTATTATTGAAAACTTTGCAGAGCTGCGCGCAGAGCTTTCAGCTAAGGGCTACAACTTTGTTTCCGTTACTGACACTGAAGTTGCCGCCACATTGCTGGCAGAAATCTACAACACCCAGGCTAATGGCGATCTGACCAAGGCTATGCAGCTTACTGGTCAGCGTCTTGAGGGTGCGTTCACCCTGCTGGCTATCCATGCTGATCATGATGATCGTATTGTTGCAGCGCGCCGTAACTCTCCTTTGGTTATTGGCTTGGGTGAAGGCGAAAACTTCCTCGGCTCTGACGTTTCTGGCTTCATCGATTACACCCGCAAGGCTGTTGAGATGGGCAACGATCAGATTGTGACCATCACTGCGAACGACTACCAGATCACCAACTTCGATGGTTCTGAGGCAACCGGAAAACCTTTCGACGTGGAGTGGGATGCGGCTGCTGCTGAAAAGGGTGGCTTTGATTCCTTCATGGATAAGGAAATCCACGACCAGCCAGCTGCAGTGCGTGACACCCTCCTCGGACGTTTAGATGAGGATGGCAAGCTGGTCCTTGATGAGCTTCGT

test/test_parsemarkers.py

@@ -0,0 +1,37 @@
+import unittest
+import vamb
+import testtools
+from pathlib import Path
+import tempfile
+import shutil
+import io
+
+
+class TestParseMarkers(unittest.TestCase):
+    def test_instantiate(self):
+        tmp = tempfile.mkdtemp()
+        tmp_path = Path(tmp)
+        shutil.rmtree(tmp)
+        markers = vamb.parsemarkers.Markers.from_files(
+            Path(testtools.DATADIR).joinpath("marker.fna"),
+            Path(testtools.PARENTDIR).joinpath("vamb").joinpath("marker.hmm"),
+            ["abc"],
+            tmp_path,
+            4,
+            None,
+        )
+        self.assertIsNotNone(markers.markers[0])
+        self.assertEqual(len(markers.markers), 1)
+        self.assertEqual(set(markers.markers[0]), {39})
+        self.assertEqual(
+            markers.refhash, vamb.vambtools.RefHasher.hash_refnames(["abc"])
+        )
+
+        buf = io.StringIO()
+        markers.save(buf)
+        buf.seek(0)
+
+        markers2 = vamb.parsemarkers.Markers.load(buf, markers.refhash)
+        self.assertEqual(len(markers.markers), len(markers2.markers))
+        self.assertEqual(set(markers.markers[0]), set(markers2.markers[0]))
+        self.assertEqual(markers.marker_names, markers2.marker_names)