def testNCOMuchHigherThanUnacceptable(self):
file = path.join(self.test_data_dir,
"test-NCO-Much-Higher-Than-Unacceptable.fasta")
files = [file]
quality_module = QualityModule(files, self.genome_size_lower_bound,
self.genome_size_upper_bound,
self.minimum_N50_value,
self.minimum_contig_length,
self.unacceptable_num_contigs)
quality_module = quality_module.create_quality_module_dataframe()
self.assertEqual(1, len(quality_module.index),
'Invalid number of rows in results')
self.assertEqual('test-NCO-Much-Higher-Than-Unacceptable',
quality_module.index[0], 'File name not equal')
self.assertEqual(
110,
quality_module['Number of Contigs Greater Than Or Equal To ' +
str(self.minimum_contig_length) + ' bp'].iloc[0],
'Number of Contigs Greater Than Or Equal To Our Minimum Contig Length Not Equal'
)
self.assertEqual('Failed', quality_module['Quality Module'].iloc[0],
'Quality result not equal')
self.assertEqual(
'Genome length is not within the acceptable length range [{},{}] ; Number of Contigs with a length greater than or equal to the minimum Contig length [{}] exceeds the acceptable number [{}]'
.format(self.genome_size_lower_bound, self.genome_size_upper_bound,
self.minimum_contig_length, self.unacceptable_num_contigs),
quality_module['Quality Module Feedback'].iloc[0],
'Quality feedback not equal')
def testNCUnacceptableByEmptyContigs(self):
file = path.join(self.test_data_dir,
"test-NC-Unacceptable-By-Empty-Contigs.fasta")
files = [file]
quality_module = QualityModule(files, self.genome_size_lower_bound,
self.genome_size_upper_bound,
self.minimum_N50_value,
self.minimum_contig_length,
self.unacceptable_num_contigs)
quality_module = quality_module.create_quality_module_dataframe()
self.assertEqual(1, len(quality_module.index),
'Invalid number of rows in results')
self.assertEqual('test-NC-Unacceptable-By-Empty-Contigs',
quality_module.index[0], 'File name not equal')
self.assertEqual(
9, quality_module['Number of Contigs Greater Than Or Equal To ' +
str(self.minimum_contig_length) + ' bp'].iloc[0],
'Number of Contigs Greater Than Or Equal To Our Minimum Contig Length Not Equal'
)
self.assertEqual('Failed', quality_module['Quality Module'].iloc[0],
'Quality result not equal')
self.assertEqual(
'Genome length is not within the acceptable length range [{},{}]'.
format(self.genome_size_lower_bound, self.genome_size_upper_bound),
quality_module['Quality Module Feedback'].iloc[0],
'Quality feedback not equal')
def testGenomeSizeExactlyMaximum(self):
file = path.join(self.test_data_dir,
"test-Genome-Size-Exactly-Maximum.fasta")
files = [file]
quality_module = QualityModule(files, self.genome_size_lower_bound,
self.genome_size_upper_bound,
self.minimum_N50_value,
self.minimum_contig_length,
self.unacceptable_num_contigs)
quality_module = quality_module.create_quality_module_dataframe()
self.assertEqual(1, len(quality_module.index),
'Invalid number of rows in results')
self.assertEqual('test-Genome-Size-Exactly-Maximum',
quality_module.index[0], 'File name not equal')
self.assertEqual(600, quality_module['Genome Length'].iloc[0],
'Genome length not equal')
self.assertEqual('Passed', quality_module['Quality Module'].iloc[0],
'Quality result not equal')
self.assertEqual('', quality_module['Quality Module Feedback'].iloc[0],
'Quality feedback not equal')
def testN50Calculation(self):
#tests to make sure N50 contig length +all contig lengths greater than it >= half of genome length, here we are testing the = part
file = path.join(self.test_data_dir, "test-N50-Calculation.fasta")
files = [file]
quality_module = QualityModule(files, self.genome_size_lower_bound,
self.genome_size_upper_bound,
self.minimum_N50_value,
self.minimum_contig_length,
self.unacceptable_num_contigs)
quality_module = quality_module.create_quality_module_dataframe()
self.assertEqual(1, len(quality_module.index),
'Invalid number of rows in results')
self.assertEqual('test-N50-Calculation', quality_module.index[0],
'File name not equal')
self.assertEqual(102, quality_module['N50 value'].iloc[0],
'N50 vlaue not equal')
self.assertEqual('Passed', quality_module['Quality Module'].iloc[0],
'Quality result not equal')
self.assertEqual('', quality_module['Quality Module Feedback'].iloc[0],
'Quality feedback not equal')
def testN50MuchLargerThanMinimumValue(self):
file = path.join(self.test_data_dir,
"test-N50-Much-Larger-Than-Minimum-Value.fasta")
files = [file]
quality_module = QualityModule(files, self.genome_size_lower_bound,
self.genome_size_upper_bound,
self.minimum_N50_value,
self.minimum_contig_length,
self.unacceptable_num_contigs)
quality_module = quality_module.create_quality_module_dataframe()
self.assertEqual(1, len(quality_module.index),
'Invalid number of rows in results')
self.assertEqual('test-N50-Much-Larger-Than-Minimum-Value',
quality_module.index[0], 'File name not equal')
self.assertEqual(1000, quality_module['N50 value'].iloc[0],
'N50 vlaue not equal')
self.assertEqual('Failed', quality_module['Quality Module'].iloc[0],
'Quality result not equal')
self.assertEqual(
'Genome length is not within the acceptable length range [{},{}]'.
format(self.genome_size_lower_bound, self.genome_size_upper_bound),
quality_module['Quality Module Feedback'].iloc[0],
'Quality feedback not equal')
def testNCOMuchLowerThanUnacceptable(self):
file = path.join(self.test_data_dir,
"test-NCO-Much-Lower-Than-Unacceptable.fasta")
files = [file]
quality_module = QualityModule(files, self.genome_size_lower_bound,
self.genome_size_upper_bound,
self.minimum_N50_value,
self.minimum_contig_length,
self.unacceptable_num_contigs)
quality_module = quality_module.create_quality_module_dataframe()
self.assertEqual(1, len(quality_module.index),
'Invalid number of rows in results')
self.assertEqual('test-NCO-Much-Lower-Than-Unacceptable',
quality_module.index[0], 'File name not equal')
self.assertEqual(
1, quality_module['Number of Contigs Greater Than Or Equal To ' +
str(self.minimum_contig_length) + ' bp'].iloc[0],
'Number of Contigs Greater Than Or Equal To Our Minimum Contig Length Not Equal'
)
self.assertEqual('Passed', quality_module['Quality Module'].iloc[0],
'Quality result not equal')
self.assertEqual('', quality_module['Quality Module Feedback'].iloc[0],
'Quality feedback not equal')
def testGenomeSizeUnaffectedByEmptyContigs(self):
file = path.join(self.test_data_dir,
"test-Genome-Size-Unaffected-By-Empty-Contigs.fasta")
files = [file]
quality_module = QualityModule(files, self.genome_size_lower_bound,
self.genome_size_upper_bound,
self.minimum_N50_value,
self.minimum_contig_length,
self.unacceptable_num_contigs)
quality_module = quality_module.create_quality_module_dataframe()
self.assertEqual(1, len(quality_module.index),
'Invalid number of rows in results')
self.assertEqual('test-Genome-Size-Unaffected-By-Empty-Contigs',
quality_module.index[0], 'File name not equal')
self.assertEqual(600, quality_module['Genome Length'].iloc[0],
'Genome length not equal')
self.assertEqual('Failed', quality_module['Quality Module'].iloc[0],
'Quality result not equal')
self.assertEqual(
'N50 value is not greater than the specified minimum value [{}]'.
format(self.minimum_N50_value),
quality_module['Quality Module Feedback'].iloc[0],
'Quality feedback not equal')
def testGenomeSizeLargerThanMaximum(self):
file = path.join(self.test_data_dir,
"test-Genome-Size-Larger-Than-Maximum.fasta")
files = [file]
quality_module = QualityModule(files, self.genome_size_lower_bound,
self.genome_size_upper_bound,
self.minimum_N50_value,
self.minimum_contig_length,
self.unacceptable_num_contigs)
quality_module = quality_module.create_quality_module_dataframe()
self.assertEqual(1, len(quality_module.index),
'Invalid number of rows in results')
self.assertEqual('test-Genome-Size-Larger-Than-Maximum',
quality_module.index[0], 'File name not equal')
self.assertEqual(700, quality_module['Genome Length'].iloc[0],
'Genome length not equal')
self.assertEqual('Failed', quality_module['Quality Module'].iloc[0],
'Quality result not equal')
self.assertEqual(
'Genome length is not within the acceptable length range [{},{}] ; N50 value is not greater than the specified minimum value [{}]'
.format(self.genome_size_lower_bound, self.genome_size_upper_bound,
self.minimum_N50_value),
quality_module['Quality Module Feedback'].iloc[0],
'Quality feedback not equal')
def create_quality_module_dataframe(self,files,genome_size_lower_bound,genome_size_upper_bound,minimum_N50_value,
minimum_contig_length,unacceptable_num_contigs) ->DataFrame:
quality_module = QualityModule(files,genome_size_lower_bound,genome_size_upper_bound,minimum_N50_value,
minimum_contig_length,unacceptable_num_contigs)
return quality_module.create_quality_module_dataframe()
