def test_renamedtemplatefile_infer_raw_name_failed_because_of_unassigned_file(
):
f = RenamedTemplateFile(name='bam_output',
regex=r'(?P<basename>.+?)_output.bam',
raw_name='{basename}.bam')
with pytest.raises(exception.FileUnassignedException):
assert f.infer_raw_name() == 'test1.bam'
def test_renamedtemplatefile_rename_command():
f = RenamedTemplateFile(name='bam_output',
regex=r'(?P<basename>.+?)_output.bam',
raw_name='{basename}.bam')
name = 'test1_output.bam'
f.assign(name)
assert f.rename_command() == 'mv test1.bam test1_output.bam'
def test_renamedtemplatefile_assign_failed_because_of_no_match():
f = RenamedTemplateFile(
name='bam_output',
regex=r'(?P<basename>.+?)_output.bam',
raw_name='{basename}.bam',
)
name = 'test1_report.bam'
with pytest.raises(exception.FileNameMismatchException):
f.assign(name)
def test_renamedtemplatefile_assign():
f = RenamedTemplateFile(
name='bam_output',
regex=r'(?P<basename>.+?)_output.bam',
raw_name='{basename}.bam',
)
name = 'test_output.bam'
f.assign(name)
assert f.filename == 'test_output.bam'
assert f.get_wildcard('basename') == 'test'
def test_renamedtemplatefile_with_multiple_group_regex():
f = RenamedTemplateFile(
name='chip_output',
regex=r'(?P<cell>.+?)_(?P<target>.+?).bam',
raw_name='{cell}_{target}_output.bam',
)
names = 'HEK293T_H3K27ac.bam'
f.assign(names)
assert f.filename == 'HEK293T_H3K27ac.bam'
assert f.get_wildcard('cell') == 'HEK293T'
assert f.get_wildcard('target') == 'H3K27ac'
assert f.infer_raw_name() == 'HEK293T_H3K27ac_output.bam'
assert f.rename_command(
) == 'mv HEK293T_H3K27ac_output.bam HEK293T_H3K27ac.bam'
def test_file_with_directory():
f = RenamedTemplateFile(
name='chip_output',
regex=r'/project/test/mapping_result/(?P<cell>.+?)_(?P<target>.+?).bam',
raw_name='/project/test/mapping_result/{cell}_{target}_output.bam',
)
bam_name = '/project/test/mapping_result/HEK293T_H3K27ac.bam'
raw_bam_name = '/project/test/mapping_result/HEK293T_H3K27ac_output.bam'
name = bam_name
f.assign(name)
assert f.filename == bam_name
assert f.get_wildcard('cell') == 'HEK293T'
assert f.get_wildcard('target') == 'H3K27ac'
assert f.infer_raw_name() == raw_bam_name
assert f.rename_command() == 'mv %s %s' % (raw_bam_name, bam_name)
def test_renamedtemplatefile_init():
f = RenamedTemplateFile(
name='bam_output',
regex=r'(?P<basename>.+?)_output.bam',
raw_name='{basename}.bam',
)