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

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"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author padge
date Fri, 25 Mar 2022 13:04:31 +0000
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-1:000000000000 0:49b058e85902
1 import pytest
2 from pathlib import Path
3
4 from Bio import AlignIO
5 from clipkit.files import get_alignment_and_format, FileFormat
6
7 here = Path(__file__)
8
9
10 class TestAutomaticFileTypeDetermination(object):
11 def test_get_alignment_and_format_when_format_is_provided(self):
12 # setup
13 in_file = f"{here.parent}/examples/simple.fa"
14 file_format = 'fasta'
15
16 # execution
17 alignment, in_file_format = get_alignment_and_format(in_file, file_format)
18
19 # check results
20 assert in_file_format == FileFormat.fasta
21 assert alignment.get_alignment_length() == 6
22
23 def test_get_alignment_and_format_when_format_is_not_provided(self):
24 # setup
25 in_file = f"{here.parent}/examples/simple.fa"
26 file_format = None
27
28 # execution
29 alignment, in_file_format = get_alignment_and_format(in_file, file_format)
30
31 # check results
32 assert in_file_format == FileFormat.fasta
33 assert alignment.get_alignment_length() == 6
34
35 def test_get_alignment_and_format_raises_error_when_file_not_known(self, mocker):
36 in_file = ""
37 file_format = None
38 mocker.patch("clipkit.files.AlignIO.read", side_effect=ValueError())
39
40 with pytest.raises(Exception) as excinfo:
41 get_alignment_and_format(in_file, file_format)
42 assert "No such file or directory" in str(excinfo.value)
43
44 def test_get_alignment_and_format_raises_error_when_detection_fails(self, mocker):
45 in_file = f"{here.parent}/examples/simple.fa"
46 file_format = None
47 mocker.patch("clipkit.files.AlignIO.read", side_effect=ValueError())
48
49 with pytest.raises(Exception) as excinfo:
50 get_alignment_and_format(in_file, file_format)
51 assert "Input file could not be read" in str(excinfo.value)