def test_construct_fasta_from_report(self):
assert not os.path.exists(self.assembly.output_assembly_fasta_path)
with self.patch_required_contigs:
self.assembly.generate_fasta()
assert os.path.exists(self.assembly.output_assembly_fasta_path)
contigs = CustomAssembly.get_contig_accessions_in_fasta(self.assembly.output_assembly_fasta_path)
# original file is empty
assert len(contigs) == 1
def test_write_ncbi_assembly_report(self):
assert not os.path.exists(self.assembly.output_assembly_report_path)
original_rows = self.assembly.assembly_report_rows
with self.patch_required_contigs:
self.assembly.generate_assembly_report()
assert os.path.exists(self.assembly.output_assembly_report_path)
headers, updated_rows = CustomAssembly._get_assembly_report(self.assembly.output_assembly_report_path)
assert len(original_rows) + 1 == len(updated_rows)
def setUp(self) -> None:
config_file = os.path.join(self.resources_folder, 'remapping_config.yml')
load_config(config_file)
assembly_accession = 'GCA_000003055.3'
assembly_report_path = os.path.join(self.resources_folder, 'GCA_000003055.3_assembly_report.txt')
assembly_fasta_path = os.path.join(self.resources_folder, 'GCA_000003055.3.fa')
self.assembly = CustomAssembly(assembly_accession, assembly_fasta_path, assembly_report_path)
self.patch_required_contigs = patch.object(
CustomAssembly, 'required_contigs',
new_callable=PropertyMock(return_value=[{'genbank': 'AY526085.1', 'refseq': 'RefSeq'}])
)
self.patch_required_contigs_none = patch.object(
CustomAssembly, 'required_contigs',
new_callable=PropertyMock(return_value=[])
)
self.current_dir = os.getcwd()
os.chdir(os.path.dirname(os.path.dirname(__file__)))
def test_write_ncbi_assembly_report_no_changes(self):
assert not os.path.exists(self.assembly.output_assembly_report_path)
original_rows = self.assembly.assembly_report_rows
with self.patch_required_contigs_none:
self.assembly.generate_assembly_report()
# No change expected
assert os.path.exists(self.assembly.output_assembly_report_path)
assert os.path.islink(self.assembly.output_assembly_report_path)
headers, updated_rows = CustomAssembly._get_assembly_report(self.assembly.output_assembly_report_path)
assert len(original_rows) == len(updated_rows)
class TestCustomAssembly(unittest.TestCase):
resources_folder = os.path.join(os.path.dirname(__file__), 'resources')
def setUp(self) -> None:
config_file = os.path.join(self.resources_folder, 'remapping_config.yml')
load_config(config_file)
assembly_accession = 'GCA_000003055.3'
assembly_report_path = os.path.join(self.resources_folder, 'GCA_000003055.3_assembly_report.txt')
assembly_fasta_path = os.path.join(self.resources_folder, 'GCA_000003055.3.fa')
self.assembly = CustomAssembly(assembly_accession, assembly_fasta_path, assembly_report_path)
self.patch_required_contigs = patch.object(
CustomAssembly, 'required_contigs',
new_callable=PropertyMock(return_value=[{'genbank': 'AY526085.1', 'refseq': 'RefSeq'}])
)
self.patch_required_contigs_none = patch.object(
CustomAssembly, 'required_contigs',
new_callable=PropertyMock(return_value=[])
)
self.current_dir = os.getcwd()
os.chdir(os.path.dirname(os.path.dirname(__file__)))
def tearDown(self) -> None:
for f in [self.assembly.output_assembly_report_path, self.assembly.output_assembly_fasta_path,
os.path.join(self.resources_folder, 'AY526085.1.fa')]:
if os.path.exists(f):
os.remove(f)
def test_assembly_report_rows(self):
first_row = {
'# Sequence-Name': 'Chr1', 'Sequence-Role': 'assembled-molecule', 'Assigned-Molecule': '1',
'Assigned-Molecule-Location/Type': 'Chromosome', 'GenBank-Accn': 'GK000001.2', 'Relationship': '=',
'RefSeq-Accn': 'AC_000158.1', 'Assembly-Unit': 'Primary Assembly', 'Sequence-Length': '158337067',
'UCSC-style-name': 'na'
}
assert self.assembly.assembly_report_rows[0] == first_row
def test_download_contig_from_ncbi(self):
self.assembly.download_contig_from_ncbi('AY526085.1')
contig_file = os.path.join(self.resources_folder, 'AY526085.1.fa')
assert os.path.exists(contig_file)
assert CustomAssembly.get_contig_accessions_in_fasta(contig_file) == ['AY526085.1']
def test_extended_report_rows(self):
last_row = {'# Sequence-Name': 'AY526085.1', 'Sequence-Role': 'scaffold', 'GenBank-Accn': 'AY526085.1',
'Relationship': '=', 'RefSeq-Accn': 'RefSeq'}
with self.patch_required_contigs:
assert self.assembly.extended_report_rows[-1] == last_row
def test_write_ncbi_assembly_report(self):
assert not os.path.exists(self.assembly.output_assembly_report_path)
original_rows = self.assembly.assembly_report_rows
with self.patch_required_contigs:
self.assembly.generate_assembly_report()
assert os.path.exists(self.assembly.output_assembly_report_path)
headers, updated_rows = CustomAssembly._get_assembly_report(self.assembly.output_assembly_report_path)
assert len(original_rows) + 1 == len(updated_rows)
def test_write_ncbi_assembly_report_no_changes(self):
assert not os.path.exists(self.assembly.output_assembly_report_path)
original_rows = self.assembly.assembly_report_rows
with self.patch_required_contigs_none:
self.assembly.generate_assembly_report()
# No change expected
assert os.path.exists(self.assembly.output_assembly_report_path)
assert os.path.islink(self.assembly.output_assembly_report_path)
headers, updated_rows = CustomAssembly._get_assembly_report(self.assembly.output_assembly_report_path)
assert len(original_rows) == len(updated_rows)
def test_construct_fasta_from_report(self):
assert not os.path.exists(self.assembly.output_assembly_fasta_path)
with self.patch_required_contigs:
self.assembly.generate_fasta()
assert os.path.exists(self.assembly.output_assembly_fasta_path)
contigs = CustomAssembly.get_contig_accessions_in_fasta(self.assembly.output_assembly_fasta_path)
# original file is empty
assert len(contigs) == 1
def test_construct_fasta_from_report_no_change(self):
assert not os.path.exists(self.assembly.output_assembly_fasta_path)
with self.patch_required_contigs_none:
self.assembly.generate_fasta()
assert os.path.exists(self.assembly.output_assembly_fasta_path)
assert os.path.islink(self.assembly.output_assembly_fasta_path)
contigs = CustomAssembly.get_contig_accessions_in_fasta(self.assembly.output_assembly_fasta_path)
# original file is empty
assert len(contigs) == 0
def test_download_contig_from_ncbi(self):
self.assembly.download_contig_from_ncbi('AY526085.1')
contig_file = os.path.join(self.resources_folder, 'AY526085.1.fa')
assert os.path.exists(contig_file)
assert CustomAssembly.get_contig_accessions_in_fasta(contig_file) == ['AY526085.1']