def test_dataset_with_gene_missing_reading_frame(self):
SAMPLE_DATA_PATH = os.path.join(
os.path.abspath(os.path.dirname(__file__)), 'sample_data.txt')
with open(SAMPLE_DATA_PATH, 'r') as handle:
sample_data = json.loads(handle.read())
data = []
append = data.append
for i in sample_data:
seq_record = SeqRecordExpanded(i['seq'],
voucher_code=i['voucher_code'],
taxonomy=i['taxonomy'],
gene_code=i['gene_code'],
reading_frame=i['reading_frame'],
table=i['table'])
if i['gene_code'] == 'ArgKin':
seq_record.reading_frame = None
append(seq_record)
self.assertRaises(ValueError,
Dataset,
data,
format='NEXUS',
codon_positions='ALL',
partitioning='1st-2nd, 3rd',
aminoacids=True)
def test_degen_standard(self):
seq_record = SeqRecordExpanded(self.seq, reading_frame=1, table=1)
expected = 'TCNGARTGGAARACNAARMGNCCN'
self.assertEqual(expected, seq_record.degenerate(), 'Using reading_frame=1')
seq_record = SeqRecordExpanded(self.seq, reading_frame=2, table=1)
expected = 'YTNAAYGGNMGNCARAGYGTNCA'
self.assertEqual(expected, seq_record.degenerate(), 'Using reading_frame=2')
def test_degen_sz(self):
seq_record = SeqRecordExpanded(self.seq, reading_frame=1)
expected = 'NNNGARTGGAARACNAARMGNCCN'
self.assertEqual(expected, seq_record.degenerate(method='SZ'), 'Using reading_frame=1')
seq_record = SeqRecordExpanded(self.seq, reading_frame=3)
expected = 'TGAATGGARGAYAARGCNNNNA'
self.assertEqual(expected, seq_record.degenerate(method='SZ'), 'Using reading_frame=3')
def test_translate_with_table_at_function_level(self):
seq = 'TCTGAATGGAAGACAAAGCGTCCA'
seq_record = SeqRecordExpanded(seq, reading_frame=1)
expected = 'SEWKTKRP'
self.assertEqual(expected, seq_record.translate(table=1))
seq = 'ACACGTCGACTCCGGCAAGTCCACTACCACAGGA'
seq_record = SeqRecordExpanded(seq, reading_frame=2)
expected = 'HVDSGKSTTTG'
self.assertEqual(expected, seq_record.translate(table=1))
def test_gapped_translation_with_mixed_codons(self):
seq = 'TCTN--GAATGGAAGACAAAGCGTCCA'
seq_record = SeqRecordExpanded(seq, reading_frame=1)
self.assertRaises(TranslationErrorMixedGappedSeq, seq_record.translate,
table=1)
try:
seq_record.translate(table=1)
except TranslationErrorMixedGappedSeq as e:
self.assertTrue("Gene" in e.__str__())
def test_getting_codon_positions_reading_frame_3(self):
seq = 'GTCGTGGGGGCCCACGTGGACGTGG'
seq_record = SeqRecordExpanded(seq, reading_frame=3)
expected = 'CGGCCGCG'
self.assertEqual(expected, seq_record.first_codon_position(), 'Fist codon position')
expected = 'GGGGCGGGG'
self.assertEqual(expected, seq_record.second_codon_position(), 'Second codon position')
expected = 'TTGCATAT'
self.assertEqual(expected, seq_record.third_codon_position(), 'Third codon position')
def test_getting_codon_positions_reading_frame_1(self):
seq = 'GAATGGAAGACAAAGTCTCGTCCA'
seq_record = SeqRecordExpanded(seq, reading_frame=1)
expected = 'GTAAATCC'
self.assertEqual(expected, seq_record.first_codon_position(), 'Fist codon position')
expected = 'AGACACGC'
self.assertEqual(expected, seq_record.second_codon_position(), 'Second codon position')
expected = 'AGGAGTTA'
self.assertEqual(expected, seq_record.third_codon_position(), 'Third codon position')
def test_getting_codon_positions_reading_frame_2(self):
seq = 'ACACGTCGACTCCGGCAAGTCCACTACCACAGGACATTTGATTTACAAATGTGGTGGTATCGACAAGCGT'
seq_record = SeqRecordExpanded(seq, reading_frame=2)
expected = 'CGGTGATAAAGCTATATGGAGAC'
self.assertEqual(expected, seq_record.first_codon_position(), 'Fist codon position')
expected = 'ATACGACCCCGATTAAGGGTAAG'
self.assertEqual(expected, seq_record.second_codon_position(), 'Second codon position')
expected = 'ACCCCCGCTCAATGTCATTTCCGT'
self.assertEqual(expected, seq_record.third_codon_position(), 'Third codon position')
def test_degenerate(self):
SAMPLE_DATA_PATH = os.path.join(
os.path.abspath(os.path.dirname(__file__)), 'sample_data.txt')
with open(SAMPLE_DATA_PATH, 'r') as handle:
sample_data = json.loads(handle.read())
data = []
append = data.append
for i in sample_data:
seq_record = SeqRecordExpanded(i['seq'],
voucher_code=i['voucher_code'],
taxonomy=i['taxonomy'],
gene_code=i['gene_code'],
reading_frame=i['reading_frame'],
table=i['table'])
append(seq_record)
with open(os.path.join(NEXUS_DATA_PATH, 'dataset_degenerated.nex'),
'r') as handle:
expected = handle.read().strip()
dataset = Dataset(data,
format='NEXUS',
codon_positions='ALL',
partitioning='by gene',
degenerate='S')
result = dataset.dataset_str
self.assertEqual(expected, result)
def test_flatten_taxonomy(self):
seq = {
'seq': '????????????',
'voucher_code': "CP100-11",
'taxonomy': {
"orden": "Lepidoptera",
"family": "Nymphalidae",
"subfamily": "Satyrinae",
"tribe": "Satyrini",
"subtribe": "Euptychiina",
"genus": "Euptychia",
"species": "",
},
'gene_code': 'ef1a',
'reading_frame': 2,
'table': 1,
}
dataset_block = DatasetBlock(data="",
codon_positions="ALL",
partitioning="")
seq_record = SeqRecordExpanded(
seq['seq'],
voucher_code=seq['voucher_code'],
taxonomy=seq['taxonomy'],
gene_code=seq['gene_code'],
reading_frame=seq['reading_frame'],
table=seq['table'],
)
expected = "_Lepidoptera_Nymphalidae_Satyrinae_Satyrini_Euptychiina_Euptychia"
result = dataset_block.flatten_taxonomy(seq_record)
self.assertEqual(expected, result)
def build_seq_obj(self, code, gene_code, accession_number, our_taxon_names, all_seqs):
"""Builds a SeqRecordExpanded object. If cannot be built, returns None.
"""
this_voucher_seqs = self.extract_sequence_from_all_seqs_in_db(all_seqs, code, gene_code)
if this_voucher_seqs == '?':
seq = '?' * self.gene_codes_metadata[gene_code]['length']
else:
seq = self.create_seq_record(this_voucher_seqs)
if code in our_taxon_names:
lineage = self.get_lineage(code)
seq_record = SeqRecordExpanded(
seq,
voucher_code=code.replace(" ", "_"),
taxonomy=our_taxon_names[code],
gene_code=gene_code,
reading_frame=self.gene_codes_metadata[gene_code]['reading_frame'],
table=self.gene_codes_metadata[gene_code]['genetic_code'],
lineage=lineage,
accession_number=accession_number,
)
return seq_record
else:
return None
def test_dataset_with_gene_missing_reading_frame(self):
SAMPLE_DATA_PATH = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'sample_data.txt')
with open(SAMPLE_DATA_PATH, 'r') as handle:
sample_data = json.loads(handle.read())
data = []
append = data.append
for i in sample_data:
seq_record = SeqRecordExpanded(i['seq'], voucher_code=i['voucher_code'],
taxonomy=i['taxonomy'], gene_code=i['gene_code'],
reading_frame=i['reading_frame'], table=i['table'])
if i['gene_code'] == 'ArgKin':
seq_record.reading_frame = None
append(seq_record)
self.assertRaises(ValueError, Dataset, data, format='NEXUS', codon_positions='ALL',
partitioning='1st-2nd, 3rd', aminoacids=True)
def test_get_seq__amino_acid_with_missing_bp_as_dash(self):
seq_record = SeqRecordExpanded('ATACGGTA-',
table=1,
reading_frame=1,
voucher_code="CP100-10",
gene_code="wingless")
result = get_seq(seq_record, codon_positions='ALL', aminoacids=True)
self.assertEqual("IRX", result.seq)
def setUp(self):
self.maxDiff = None
with open(SAMPLE_DATA_PATH, 'r') as handle:
sample_data = json.loads(handle.read())
self.data = []
append = self.data.append
for i in sample_data:
seq_record = SeqRecordExpanded(i['seq'], voucher_code=i['voucher_code'],
taxonomy=i['taxonomy'], gene_code=i['gene_code'],
reading_frame=i['reading_frame'], table=i['table'])
append(seq_record)
def test_dataset_when_seqrecord_taxonomy_is_none(self):
raw_data = get_test_data('raw_data')
raw_data[0]['taxonomy'] = None
seq_records = []
for i in raw_data:
seq_record = SeqRecordExpanded(i['seq'],
voucher_code=i['voucher_code'],
taxonomy=i['taxonomy'],
gene_code=i['gene_code'],
reading_frame=i['reading_frame'],
table=i['table'])
seq_records.append(seq_record)
dataset = Dataset(seq_records, format='NEXUS', partitioning='by gene')
self.assertTrue('CP100_10 ' in dataset.dataset_str)
def get_test_data(filename="sample_data.txt"):
SAMPLE_DATA_PATH = os.path.join(os.path.abspath(os.path.dirname(__file__)),
filename)
with open(SAMPLE_DATA_PATH, 'r') as handle:
sample_data = json.loads(handle.read())
data = []
append = data.append
for i in sample_data:
seq_record = SeqRecordExpanded(i['seq'],
voucher_code=i['voucher_code'],
taxonomy=i['taxonomy'],
gene_code=i['gene_code'],
reading_frame=i['reading_frame'],
table=i['table'])
append(seq_record)
return data
def test_dataset_when_seqrecord_taxonomy_is_has_family(self):
raw_data = get_test_data('raw_data')
raw_data[0]['taxonomy'] = {
'family': 'Aussidae',
'genus': 'Aus',
'species': 'aus'
}
seq_records = []
for i in raw_data:
seq_record = SeqRecordExpanded(i['seq'],
voucher_code=i['voucher_code'],
taxonomy=i['taxonomy'],
gene_code=i['gene_code'],
reading_frame=i['reading_frame'],
table=i['table'])
seq_records.append(seq_record)
dataset = Dataset(seq_records, format='NEXUS', partitioning='by gene')
self.assertTrue('CP100_10_Aussidae_Aus_aus ' in dataset.dataset_str)
def test_translate(self):
seq = 'TCTGAATGGAAGACAAAGCGTCCA'
seq_record = SeqRecordExpanded(seq, reading_frame=1, table=1)
expected = 'SEWKTKRP'
self.assertEqual(expected, seq_record.translate(), 'Using reading_frame=1')
seq = 'TCTGAATGGAA?ACAAAGCGT???'
seq_record = SeqRecordExpanded(seq, reading_frame=1, table=1)
expected = 'SEWXTKRX'
self.assertEqual(expected, seq_record.translate(), 'Using reading_frame=1')
seq = 'ACACGTCGACTCCGGCAAGTCCACTACCACAGGA'
seq_record = SeqRecordExpanded(seq, reading_frame=2, table=1)
expected = 'HVDSGKSTTTG'
self.assertEqual(expected, seq_record.translate(), 'Using reading_frame=2')
def get_test_data(type_of_data=None, filename="sample_data.txt"):
"""
Parameters:
type_of_data (str): ``raw_data`` or ``seq_records``
"""
with open(os.path.join(NEXUS_DATA_PATH, "..", filename), "r") as handle:
raw_data = json.loads(handle.read())
if type_of_data == 'raw_data':
return raw_data
elif type_of_data == 'seq_records':
seq_records = []
for i in raw_data:
seq_record = SeqRecordExpanded(i['seq'],
voucher_code=i['voucher_code'],
taxonomy=i['taxonomy'],
gene_code=i['gene_code'],
reading_frame=i['reading_frame'],
table=i['table'])
seq_records.append(seq_record)
return seq_records
def test_flatten_taxonomy__no_taxonomy(self):
seq = {
'seq': '????????????',
'voucher_code': "CP100-11",
'gene_code': 'ef1a',
'reading_frame': 2,
'table': 1,
}
dataset_block = DatasetBlock(data="",
codon_positions="ALL",
partitioning="")
seq_record = SeqRecordExpanded(
seq['seq'],
voucher_code=seq['voucher_code'],
gene_code=seq['gene_code'],
reading_frame=seq['reading_frame'],
table=seq['table'],
)
expected = ""
result = dataset_block.flatten_taxonomy(seq_record)
self.assertEqual(expected, result)
def build_seq_obj(self, code, gene_code, our_taxon_names, all_seqs):
"""Builds a SeqRecordExpanded object. I cannot be built, returns None.
"""
this_voucher_seqs = self.extract_sequence_from_all_seqs_in_db(all_seqs, code, gene_code)
if this_voucher_seqs == '?':
seq = '?' * self.gene_codes_metadata[gene_code]['length']
else:
seq = self.create_seq_record(this_voucher_seqs)
seq_record = SeqRecordExpanded(seq)
if code in our_taxon_names:
seq_record.voucher_code = code
seq_record.taxonomy = our_taxon_names[code]
seq_record.gene_code = gene_code
seq_record.reading_frame = self.gene_codes_metadata[gene_code]['reading_frame']
seq_record.table = self.gene_codes_metadata[gene_code]['genetic_code']
return seq_record
else:
return None
def setUp(self):
self.seq_record = SeqRecordExpanded('ATACGGTAG',
table=1,
reading_frame=1,
voucher_code="CP100-10",
gene_code="wingless")
def test_sorting_seq_records(self):
"""Test SeqRecordExpanded objects are sorted by gene_code and then by
voucher_code.
"""
my_list = [
{
'seq':
'CTgCacGgTCaagacGTGCtGgaTgaggctGccGacTTttcggtCtGTAgGCGACGCCTTGAAGGACGGCTTCGACGGAGCGTCGCGGGTTATGATGCCCAATACGGAGTTGGAAGCACCAGCTCAGCGAAACGATGCCGCTCCGCACAGAGTCCCGCGACGAGACCGATACAGATTTCAACTwCGGCCGCACAATCCTGACCACAAAACACCCGGAGTCAAGGACCTAGTGTACTTGGAATCATCGCCGGGTTTCTGCGAAAAGAACCCGCGGCTGGGCATTCCAGGCACGCACGGGCGTTCCTGCAATGACACGAGTATCGGCGTCGACGGCTGCGACCTCATGTGCTGTGGCCGTGGCTACCGGACCGAGACAATGTTCGTTGTGGAGCGATGCAAC',
'voucher_code': "CP100-11",
'taxonomy': {
'genus': 'Aus',
'species': 'bus'
},
'gene_code': 'wingless',
'reading_frame': 2,
'table': 1
},
{
'seq':
'???????????????????????????????????????????TCTGTAGGCGATGCCTTGAAGGACGGCTTCGACGGAGCGTCGCGGGTCATGATGCCCAATACGGAGTTAGAAGCGCCTGCTCAGCGAAACGACGCCGCCCCGCACAGAGTCCCGCGACGAGACCGATACAGATTTCAACTTCGGCCGCACAATCCTGACCACAAAACACCCGGA?TCAAGGACCTAGTGTACTTGGAATCATCGCCGGGTTTCTGCGAAAAGAACCCGCGGCTGGGCATTCCCGGCACGCACGGGCGTGCCTGCAACGACACGAGTATCGGCGTCGACGGCTGCGACCTCATGTGCTGCGGCCGTGGCTACCGGACCGAGACAATGTTCGTCGTGGAGCGATGCAAC',
'voucher_code': "CP100-10",
'taxonomy': {
'genus': 'Aus',
'species': 'aus'
},
'gene_code': 'wingless',
'reading_frame': 2,
'table': 1
},
{
'seq':
'???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????',
'voucher_code': "CP100-11",
'taxonomy': {
'genus': 'Aus',
'species': 'bus'
},
'gene_code': 'RpS2',
'reading_frame': 3,
'table': 1
},
{
'seq':
'???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????',
'voucher_code': "CP100-10",
'taxonomy': {
'genus': 'Aus',
'species': 'aus'
},
'gene_code': 'RpS2',
'reading_frame': 3,
'table': 1
},
{
'seq':
'??????????????????????????????????????????????????????????????????????????AAAAAGAAACTTTTGGAAATTTaggtataATTTATGCTATATTAGCAATTGGATTATTAGGATTTATTGTGTGAGCTCATCATATATTTACTGTAGGTATAGATATTGATACTCGAGCTTATTTTACCTCTGCTACAATAATTATTGCAGTCCCAACAGGAATTAAAATTTTTAGTTGATTAGCAACTCTACATGGAACACAAATTAATTATAGTCCTTCCATACTTTGAAGACTAGGATTTATTTTTTTATTTACAGTAGGAGGATTAACTGGTGTAATTTTAGCTAATTCTTCAATTGATATTGCTCTTCATGATACTTATTATGTAgTAgCCCACTTTCATTATGTATTGTCTATAGGAGCAGTATTTGCTATTTTTGGAGGATTTGTCCATTGATATCCTTTATTTACAGGATTAATATTAAATCCATATTTATTAAAAATTCAATTTATTTCAATATTTATTGGAGTTAACTTAACTTTTTTCCCACAACATTTTTTAGGTTTAGCTGGTATACCTCGACGTTACTCAGATTACCCAGATAATTTTTTATCTTGAAATATTATTTCATCATTAGGATCTTATATTTCTCTATTTTCTATAATAATAATAaTTATTATTATATGAGAATCAATAACTTATCAACGTATAATTTTATTTTCATTAAATATACctTCTTCAATTGAGTGATATCAAAAaTTACCACCTGCCGAACATTCTTATAAtGAAC',
'voucher_code': "CP100-10",
'taxonomy': {
'genus': 'Aus',
'species': 'aus'
},
'gene_code': 'COI_end',
'reading_frame': 2,
'table': 5
},
{
'seq':
'?????????????????????????????????????????????????????????????????????????AAAAAAGAAACTTTCGGAAGCTTAGGTATAATTTACGCTATATTAGCTATTGGATTATTAGGATtTATTGTATGAGCTCATCATATATTTACAGTAGGAATAGATATTGATACCCGAGCTTATTTTACTTCTGCTACAATAATTATTGCCGTACCAACAGGAATTAAAATTTTTAGCTGATTAGCAACTCTTCACGGAACTCAAATCAATTATAGTCCTTCCATACTTTGAAGATTAGGATTTATTTTTTTATTTACAGTAGGAGGACTAACTGGTGTAATTTTAGCTAATTCTTCAATTGATATTACTCTCCATGATACTTATTATGTTGTAGCTCATTTTCATTATGTTCTATCTATAGGAGCAGTATTTGCTATTTTCGGAGGATTTATCCACTGATACCCCTTATTTACAGGATTAATATTAAACCCATATTTATTAAAAATTCAATTCATTTCAATATTTATTGGAGTTAATTTAACTTTTTTTCCACAACATTTTTTAGGGTTAGCTGGTATACCTCGTCGTTATTCAGATTACCCAGATAATTTTTTATCTTGAAATATTATTTCATCATTAGGATCTTATATTTCATTATTTTCTATAATAATAATAATTATTATTATTTGAGAATCAATAATTTATCAACGTATAATTTTATTTACATTAAATATACCCTCTTCAATTGAATGATATCAAAATTTACCTCCTGCCGAACATTCTTATAATGAAC',
'voucher_code': "CP100-11",
'taxonomy': {
'genus': 'Aus',
'species': 'bus'
},
'gene_code': 'COI_end',
'reading_frame': 2,
'table': 5
},
{
'seq':
'????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????',
'voucher_code': "CP100-10",
'taxonomy': {
'genus': 'Aus',
'species': 'aus'
},
'gene_code': 'ef1a',
'reading_frame': 2,
'table': 1
},
{
'seq':
'????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????',
'voucher_code': "CP100-11",
'taxonomy': {
'genus': 'Aus',
'species': 'bus'
},
'gene_code': 'ef1a',
'reading_frame': 2,
'table': 1
},
]
seq_records = []
append = seq_records.append
for i in my_list:
seq_record = SeqRecordExpanded(
i['seq'],
voucher_code=i['voucher_code'],
taxonomy=i['taxonomy'],
gene_code=i['gene_code'],
reading_frame=i['reading_frame'],
table=i['table'],
)
append(seq_record)
expected = [
'COI_end', 'COI_end', 'ef1a', 'ef1a', 'RpS2', 'RpS2', 'wingless',
'wingless'
]
result = Dataset(seq_records).seq_records
self.assertEqual(expected, [i.gene_code for i in result])
expected = [
'CP100_10', 'CP100_11', 'CP100_10', 'CP100_11', 'CP100_10',
'CP100_11', 'CP100_10', 'CP100_11'
]
self.assertEqual(expected, [i.voucher_code for i in result])
def test_getting_first_and_second_codon_positions_reading_frame_1(self):
seq = 'GAATGGAAGACAAAGTCTCGTCCA'
seq_record = SeqRecordExpanded(seq, reading_frame=1)
expected = 'GATGAAACAATCCGCC'
self.assertEqual(expected, seq_record.first_and_second_codon_positions())
def test_degen_z(self):
seq_record = SeqRecordExpanded(self.seq, reading_frame=1)
expected = 'TCNGARTGGAARACNAARMGNCCN'
self.assertEqual(expected, seq_record.degenerate(method='Z'))
def test_gapped_translation(self):
seq = 'TCT---GAATGGAAGACAAAGCGTCCA'
seq_record = SeqRecordExpanded(seq, reading_frame=1)
expected = 'S-EWKTKRP'
self.assertEqual(expected, seq_record.translate(table=1))
