diff clipkit_repo/tests/unit/test_files.py @ 0:49b058e85902 draft

"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clipkit_repo/tests/unit/test_files.py	Fri Mar 25 13:04:31 2022 +0000
@@ -0,0 +1,51 @@
+import pytest
+from pathlib import Path
+
+from Bio import AlignIO
+from clipkit.files import get_alignment_and_format, FileFormat
+
+here = Path(__file__)
+
+
+class TestAutomaticFileTypeDetermination(object):
+    def test_get_alignment_and_format_when_format_is_provided(self):
+        # setup
+        in_file = f"{here.parent}/examples/simple.fa"
+        file_format = 'fasta'
+
+        # execution
+        alignment, in_file_format = get_alignment_and_format(in_file, file_format)
+
+        # check results
+        assert in_file_format == FileFormat.fasta
+        assert alignment.get_alignment_length() == 6
+
+    def test_get_alignment_and_format_when_format_is_not_provided(self):
+        # setup
+        in_file = f"{here.parent}/examples/simple.fa"
+        file_format = None
+
+        # execution
+        alignment, in_file_format = get_alignment_and_format(in_file, file_format)
+
+        # check results
+        assert in_file_format == FileFormat.fasta
+        assert alignment.get_alignment_length() == 6
+
+    def test_get_alignment_and_format_raises_error_when_file_not_known(self, mocker):
+        in_file = ""
+        file_format = None
+        mocker.patch("clipkit.files.AlignIO.read", side_effect=ValueError())
+
+        with pytest.raises(Exception) as excinfo:
+            get_alignment_and_format(in_file, file_format)
+        assert "No such file or directory" in str(excinfo.value)
+
+    def test_get_alignment_and_format_raises_error_when_detection_fails(self, mocker):
+        in_file = f"{here.parent}/examples/simple.fa"
+        file_format = None
+        mocker.patch("clipkit.files.AlignIO.read", side_effect=ValueError())
+
+        with pytest.raises(Exception) as excinfo:
+            get_alignment_and_format(in_file, file_format)
+        assert "Input file could not be read" in str(excinfo.value)