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