add some tests for plugins

countess/plugins/mutagenize.py

@@ -24,7 +24,7 @@ def mutagenize(
  yield sequence[0:n] + b2 + sequence[n:], n + 1, None, b2
  if delete:
  yield sequence[0:n] + sequence[n + 1 :], n + 1, b1, None
- if del3:
+ if del3 and n+3 <= len(sequence):
  yield sequence[0:n] + sequence[n + 3 :], n + 1, sequence[n : n + 3], None
  if ins3:
  for ins in product("ACGT", "ACGT", "ACGT"):

countess/plugins/variant.py

@@ -21,7 +21,6 @@ class VariantPlugin(PandasTransformDictToSinglePlugin):
  "column": ColumnChoiceParam("Input Column", "sequence"),
  "reference": ColumnOrNoneChoiceParam("Reference Column"),
  "sequence": StringParam("*OR* Reference Sequence"),
- "auto": BooleanParam("Automatic Reference Sequence?", False),
  "output": StringParam("Output Column", "variant"),
  "max_mutations": IntegerParam("Max Mutations", 10),
  "drop": BooleanParam("Drop unidentified variants", False),

tests/plugins/test_csv.py

@@ -0,0 +1,20 @@
+import pytest
+
+import pandas as pd
+
+from countess.plugins.csv import LoadCsvPlugin
+from countess.core.logger import MultiprocessLogger
+
+logger = MultiprocessLogger()
+
+def test_load_csv():
+
+ plugin = LoadCsvPlugin()
+
+ plugin.set_parameter('files.0.filename', 'tests/input1.csv')
+
+
+ output_df = next(plugin.load_file(0, logger))
+
+ assert list(output_df.columns) == ['thing', 'count']
+ assert len(output_df) == 4

tests/plugins/test_mutagenize.py

@@ -0,0 +1,122 @@
+import pytest
+
+import pandas as pd
+
+from countess.plugins.mutagenize import MutagenizePlugin
+from countess.core.logger import MultiprocessLogger
+
+logger = MultiprocessLogger()
+
+def test_mutagenize_mutate():
+
+ plugin = MutagenizePlugin()
+ plugin.set_parameter('sequence', 'GATTACA')
+ plugin.set_parameter('mutate', True)
+
+ output_df = next(plugin.load_file(0, logger))
+ output = list(output_df['sequence'])
+
+ assert len(output) == 21
+
+
+def test_mutagenize_insert():
+
+ plugin = MutagenizePlugin()
+ plugin.set_parameter('sequence', 'GATTACA')
+ plugin.set_parameter('mutate', False)
+ plugin.set_parameter('insert', True)
+
+ output_df = next(plugin.load_file(0, logger))
+ output = list(output_df['sequence'])
+
+ assert len(output) == 32
+
+
+def test_mutagenize_insert3():
+
+ plugin = MutagenizePlugin()
+ plugin.set_parameter('sequence', 'GATTACA')
+ plugin.set_parameter('mutate', False)
+ plugin.set_parameter('ins3', True)
+
+ output_df = next(plugin.load_file(0, logger))
+ output = list(output_df['sequence'])
+
+ assert len(output) == 512
+
+def test_mutagenize_insert_dedup():
+
+ plugin = MutagenizePlugin()
+ plugin.set_parameter('sequence', 'GATTACA')
+ plugin.set_parameter('mutate', False)
+ plugin.set_parameter('insert', True)
+ plugin.set_parameter('remove', True)
+
+ output_df = next(plugin.load_file(0, logger))
+
+ assert len(output_df) == 25
+
+
+def test_mutagenize_insert3_dedup():
+
+ plugin = MutagenizePlugin()
+ plugin.set_parameter('sequence', 'GATTACA')
+ plugin.set_parameter('mutate', False)
+ plugin.set_parameter('ins3', True)
+ plugin.set_parameter('remove', True)
+
+ output_df = next(plugin.load_file(0, logger))
+
+ assert len(output_df) == 400
+
+def test_mutagenize_delete():
+
+ plugin = MutagenizePlugin()
+ plugin.set_parameter('sequence', 'GATTACA')
+ plugin.set_parameter('mutate', False)
+ plugin.set_parameter('delete', True)
+
+ output_df = next(plugin.load_file(0, logger))
+ output = list(output_df['sequence'])
+
+ assert len(output) == 7
+
+
+def test_mutagenize_del3():
+
+ plugin = MutagenizePlugin()
+ plugin.set_parameter('sequence', 'GATTACA')
+ plugin.set_parameter('mutate', False)
+ plugin.set_parameter('del3', True)
+
+ output_df = next(plugin.load_file(0, logger))
+ output = list(output_df['sequence'])
+
+ assert len(output) == 5
+
+def test_mutagenize_delete_dedup():
+
+ plugin = MutagenizePlugin()
+ plugin.set_parameter('sequence', 'GATTACA')
+ plugin.set_parameter('mutate', False)
+ plugin.set_parameter('delete', True)
+ plugin.set_parameter('remove', True)
+
+ output_df = next(plugin.load_file(0, logger))
+
+ assert len(output_df) == 6
+
+
+def test_mutagenize_del3_dedup():
+
+ plugin = MutagenizePlugin()
+ plugin.set_parameter('sequence', 'GATTACA')
+ plugin.set_parameter('mutate', False)
+ plugin.set_parameter('del3', True)
+ plugin.set_parameter('remove', True)
+
+ output_df = next(plugin.load_file(0, logger))
+
+ assert len(output_df) == 4
+
+

tests/plugins/test_variant.py

@@ -0,0 +1,29 @@
+import pytest
+
+import pandas as pd
+
+from countess.plugins.variant import VariantPlugin
+from countess.core.logger import MultiprocessLogger
+
+logger = MultiprocessLogger()
+
+def test_variant_ref_column():
+
+ input_df = pd.DataFrame([
+ { 'ref': 'TACACACAG', 'seq': 'TACAGACAG' },
+ { 'ref': 'ATGGTTGGTTC', 'seq': "ATGGTTGGTGGTTCG" }
+ ])
+
+ plugin = VariantPlugin()
+ plugin.set_parameter('column', 'seq')
+ plugin.set_parameter('reference', 'ref')
+ plugin.set_parameter('output', 'out')
+
+ plugin.prepare(['test'], None)
+
+ output_df = plugin.process_dataframe(input_df, logger)
+
+ output = output_df.to_records()
+
+ assert output[0]['out'] == 'g.5C>G'
+ assert output[1]['out'] == 'g.[7_9dup;11_12insG]'