def setUp(self):
args = []
opts = {'dumpfile': settings.MEDIA_ROOT + 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
blast_type = 'local'
voucher_code = 'CP100-10'
gene_code = 'COI'
self.blast = BLAST(blast_type, voucher_code, gene_code)
self.seq_file = ''
def test_create_blast_db_unmasked(self):
blast_type = 'local'
voucher_code = 'CP100-10'
gene_code = 'COI'
blast = BLAST(blast_type, voucher_code, gene_code, mask=False)
blast.save_seqs_to_file()
blast.create_blast_db()
files = glob.glob(
os.path.join(settings.BASE_DIR,
'..',
'core',
'db',
'COI_seqs.fas.n*')
)
self.assertTrue(len(files) > 0)
self.remove_blast_data_files()
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
blast_type = 'local'
voucher_code = 'CP100-10'
gene_code = 'COI'
self.blast = BLAST(blast_type, voucher_code, gene_code)
self.seq_file = ''
def test_create_blast_db_unmasked(self):
blast_type = 'local'
voucher_code = 'CP100-10'
gene_code = 'COI'
blast = BLAST(blast_type, voucher_code, gene_code, mask=False)
blast.save_seqs_to_file()
blast.create_blast_db()
files = glob.glob(
os.path.join(settings.BASE_DIR, '..', 'core', 'db',
'COI_seqs.fas.n*'))
self.assertTrue(len(files) > 0)
self.remove_blast_data_files()
def index(request, voucher_code, gene_code):
version, stats = get_version_stats()
username = get_username(request)
blast = BLAST('local', voucher_code, gene_code)
blast.save_seqs_to_file()
if not blast.is_blast_db_up_to_date():
blast.create_blast_db()
blast.save_query_to_file()
blast.do_blast()
result = blast.parse_blast_output()
blast.delete_query_output_files()
return render(request, 'blast_local/index.html',
{
'username': username,
'result': result,
'version': version,
'stats': stats,
},
)
def index(request: HttpRequest, voucher_code: str,
gene_code: str) -> HttpResponse:
"""Runs a local blast for voucher code and gene code
Show results to user in a table
"""
blast = BLAST('local', voucher_code, gene_code)
blast.save_seqs_to_file()
if not blast.is_blast_db_up_to_date():
try:
blast.create_blast_db()
except CalledProcessError:
log.warning("there are no sequences for gene %s", gene_code)
was_sequence_saved = blast.save_query_to_file()
if was_sequence_saved:
blast.do_blast()
result = blast.parse_blast_output()
blast.delete_query_output_files()
else:
result = {
"error": "Query sequence has no valid codons, only question marks",
}
context = get_context(request)
context["result"] = result
return render(request, 'blast_local/index.html', context)
class BlastLocalTest(TestCase):
def setUp(self):
args = []
opts = {'dumpfile': settings.MEDIA_ROOT + 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
blast_type = 'local'
voucher_code = 'CP100-10'
gene_code = 'COI'
self.blast = BLAST(blast_type, voucher_code, gene_code)
self.seq_file = ''
def remove_blast_data_files(self):
path = os.path.join(settings.MEDIA_ROOT,
'db',
'*',
)
for file in glob.glob(path):
if not file.endswith('py') and os.path.isfile(file):
os.remove(file)
def test_have_blast_db(self):
self.remove_blast_data_files()
result = self.blast.have_blast_db()
self.assertEqual(False, result)
def test_have_blast_db_true(self):
self.blast.save_seqs_to_file()
self.blast.create_blast_db()
result = self.blast.have_blast_db()
self.assertEqual(True, result)
self.remove_blast_data_files()
def test_save_seqs_to_file(self):
self.blast.save_seqs_to_file()
self.seq_file = os.path.join(settings.MEDIA_ROOT,
'db',
'COI_seqs.fas',
)
result = os.path.isfile(self.seq_file)
self.assertTrue(result)
self.remove_blast_data_files()
def test_create_blast_db(self):
blast_type = 'local'
voucher_code = 'CP100-10'
gene_code = 'COI'
blast = BLAST(blast_type, voucher_code, gene_code, mask=True)
blast.save_seqs_to_file()
blast.create_blast_db()
files = glob.glob(
os.path.join(settings.MEDIA_ROOT,
'db',
'COI_seqs.fas.n*')
)
self.assertTrue(len(files) > 0)
self.remove_blast_data_files()
def test_create_blast_db_unmasked(self):
blast_type = 'local'
voucher_code = 'CP100-10'
gene_code = 'COI'
blast = BLAST(blast_type, voucher_code, gene_code, mask=False)
blast.save_seqs_to_file()
blast.create_blast_db()
files = glob.glob(
os.path.join(settings.MEDIA_ROOT,
'db',
'COI_seqs.fas.n*')
)
self.assertTrue(len(files) > 0)
self.remove_blast_data_files()
def test_is_blast_db_up_to_date(self):
self.blast.save_seqs_to_file()
self.blast.create_blast_db()
result = self.blast.is_blast_db_up_to_date()
self.assertTrue(result)
self.remove_blast_data_files()
def test_is_blast_db_up_to_date_false(self):
self.blast.save_seqs_to_file()
self.blast.create_blast_db()
b = Vouchers.objects.get(code='CP100-10')
tomorrow = datetime.datetime.now() + datetime.timedelta(days=1)
Sequences.objects.filter(code=b, gene_code='COI').update(
time_edited=tomorrow
)
result = self.blast.is_blast_db_up_to_date()
self.assertFalse(result)
self.remove_blast_data_files()
def test_is_blast_db_up_to_date_false2(self):
self.blast.save_seqs_to_file()
result = self.blast.is_blast_db_up_to_date()
self.assertFalse(result)
self.remove_blast_data_files()
def test_do_blast(self):
self.blast.save_seqs_to_file()
self.blast.create_blast_db()
self.blast.save_query_to_file()
result = self.blast.do_blast()
self.assertTrue(os.path.isfile(result))
self.remove_blast_data_files()
def test_parse_blast_output(self):
self.blast.save_seqs_to_file()
self.blast.create_blast_db()
self.blast.save_query_to_file()
self.blast.do_blast()
result = self.blast.parse_blast_output()
self.assertTrue(611 in [i['query_length'] for i in result])
self.remove_blast_data_files()
def test_strip_question_marks(self):
seq = '?G?A??????TTTTATTTTTGG???????????????????????????????????????????CGAA??GAATTAGGTAACCCAGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACTGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAATTCCTTTAATACTTGGAGCTCCTGATATAGCTTTCCCTCGAATAAATAATATAAGATTTTGACTTCTCCCCCCCTCTTTAATTTTATTAATTTCTAGAAGAATTGTAGAAACTGGGGCCGGAACAGGCTGAACAGTATACCCTCCTTTATCTTCAAATATTGCTCATGGGGGAGCTTCTGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCAATTAATTTTATTACAACTATTATTAATATACGAATTAGTAATATATCATTTGATCAAATACCTTTATTTGTTTGATCAGTAGGAATTACAGCTTTATTATTACTTTTATCTTTACCTGTATTAGCTGGAGCTATTACCATATTATTAACGGATCGAAATTTAAATACTTCATTTTTTGACCCTGCTGGAGGAGGAGATCCCATTCTTTATCAACATCTATTTTGATTTTTTGG'
expected = 'GNANNNNNNTTTTATTTTTGGNNNNNNNNN'
result = self.blast.strip_question_marks(seq)
self.assertTrue(result.startswith(expected))
seq = '?GGAAGAATTAGGTAACCCAGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACTGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAATTCCTTTAATACTTGGAGCTCCTGATATAGCTTTCCCTCGAATAAATAATATAAGATTTTGACTTCTCCCCCCCTCTTTAATTTTATTAATTTCTAGAAGAATTGTAGAAACTGGGGCCGGAACAGGCTGAACAGTATACCCTCCTTTATCTTCAAATATTGCTCATGGGGGAGCTTCTGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCAATTAATTTTATTACAACTATTATTAATATACGAATTAGTAATATATCATTTGATCAAATACCTTTATTTGTTTGATCAGTAGGAATTACAGCTTTATTATTACTTTTATCTTTACCTGTATTAGCTGGAGCTATTACCATATTATTAACGGATCGAAATTTAAATACTTCATTTTTTGACCCTGCTGGAGGAGGAGATCCCATTCTTTATCAACATCTATTTTGATTTTTTGG'
expected = 'GGAAGAATTAGGTAACCCAGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACTGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAATTCCTTTAATACTTGGAGCTCCTGATATAGCTTTCCCTCGAATAAATAATATAAGATTTTGACTTCTCCCCCCCTCTTTAATTTTATTAATTTCTAGAAGAATTGTAGAAACTGGGGCCGGAACAGGCTGAACAGTATACCCTCCTTTATCTTCAAATATTGCTCATGGGGGAGCTTCTGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCAATTAATTTTATTACAACTATTATTAATATACGAATTAGTAATATATCATTTGATCAAATACCTTTATTTGTTTGATCAGTAGGAATTACAGCTTTATTATTACTTTTATCTTTACCTGTATTAGCTGGAGCTATTACCATATTATTAACGGATCGAAATTTAAATACTTCATTTTTTGACCCTGCTGGAGGAGGAGATCCCATTCTTTATCAACATCTATTTTGATTTTTTGG'
result = self.blast.strip_question_marks(seq)
self.assertEqual(expected, result)
def index(request: HttpRequest, voucher_code: str, gene_code: str) -> HttpResponse:
"""Runs a local blast for voucher code and gene code
Show results to user in a table
"""
blast = BLAST('local', voucher_code, gene_code)
blast.save_seqs_to_file()
if not blast.is_blast_db_up_to_date():
try:
blast.create_blast_db()
except CalledProcessError:
log.warning("there are no sequences for gene %s", gene_code)
was_sequence_saved = blast.save_query_to_file()
if was_sequence_saved:
blast.do_blast()
result = blast.parse_blast_output()
blast.delete_query_output_files()
else:
result = {
"error": "Query sequence has no valid codons, only question marks",
}
context = get_context(request)
context["result"] = result
return render(request, 'blast_local/index.html', context)
class BlastLocalTest(TestCase):
def setUp(self):
args = []
opts = {'dumpfile': 'test_db_dump.xml', 'verbosity': 0}
cmd = 'migrate_db'
call_command(cmd, *args, **opts)
blast_type = 'local'
voucher_code = 'CP100-10'
gene_code = 'COI'
self.blast = BLAST(blast_type, voucher_code, gene_code)
self.seq_file = ''
def remove_blast_data_files(self):
path = os.path.join(settings.BASE_DIR,
'..',
'core',
'db',
'*',
)
for file in glob.glob(path):
if not file.endswith('py') and os.path.isfile(file):
os.remove(file)
def test_have_blast_db(self):
self.remove_blast_data_files()
result = self.blast.have_blast_db()
self.assertEqual(False, result)
def test_have_blast_db_true(self):
self.blast.save_seqs_to_file()
self.blast.create_blast_db()
result = self.blast.have_blast_db()
self.assertEqual(True, result)
self.remove_blast_data_files()
def test_save_seqs_to_file(self):
self.blast.save_seqs_to_file()
self.seq_file = os.path.join(settings.BASE_DIR,
'..',
'core',
'db',
'COI_seqs.fas',
)
result = os.path.isfile(self.seq_file)
self.assertTrue(result)
self.remove_blast_data_files()
def test_create_blast_db(self):
blast_type = 'local'
voucher_code = 'CP100-10'
gene_code = 'COI'
blast = BLAST(blast_type, voucher_code, gene_code, mask=True)
blast.save_seqs_to_file()
blast.create_blast_db()
files = glob.glob(
os.path.join(settings.BASE_DIR,
'..',
'core',
'db',
'COI_seqs.fas.n*')
)
self.assertTrue(len(files) > 0)
self.remove_blast_data_files()
def test_create_blast_db_unmasked(self):
blast_type = 'local'
voucher_code = 'CP100-10'
gene_code = 'COI'
blast = BLAST(blast_type, voucher_code, gene_code, mask=False)
blast.save_seqs_to_file()
blast.create_blast_db()
files = glob.glob(
os.path.join(settings.BASE_DIR,
'..',
'core',
'db',
'COI_seqs.fas.n*')
)
self.assertTrue(len(files) > 0)
self.remove_blast_data_files()
def test_is_blast_db_up_to_date(self):
self.blast.save_seqs_to_file()
self.blast.create_blast_db()
result = self.blast.is_blast_db_up_to_date()
self.assertTrue(result)
self.remove_blast_data_files()
def test_is_blast_db_up_to_date_false(self):
self.blast.save_seqs_to_file()
self.blast.create_blast_db()
b = Vouchers.objects.get(code='CP100-10')
tomorrow = datetime.datetime.now() + datetime.timedelta(days=1)
Sequences.objects.filter(code=b, gene_code='COI').update(
time_edited=tomorrow
)
result = self.blast.is_blast_db_up_to_date()
self.assertFalse(result)
self.remove_blast_data_files()
def test_is_blast_db_up_to_date_false2(self):
self.blast.save_seqs_to_file()
result = self.blast.is_blast_db_up_to_date()
self.assertFalse(result)
self.remove_blast_data_files()
def test_do_blast(self):
self.blast.save_seqs_to_file()
self.blast.create_blast_db()
self.blast.save_query_to_file()
result = self.blast.do_blast()
self.assertTrue(os.path.isfile(result))
self.remove_blast_data_files()
def test_parse_blast_output(self):
self.blast.save_seqs_to_file()
self.blast.create_blast_db()
self.blast.save_query_to_file()
self.blast.do_blast()
result = self.blast.parse_blast_output()
self.assertTrue(611 in [i['query_length'] for i in result])
self.remove_blast_data_files()
def test_strip_question_marks(self):
seq = '?G?A??????TTTTATTTTTGG???????????????????????????????????????????CGAA??GAATTAGGTAACCCAGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACTGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAATTCCTTTAATACTTGGAGCTCCTGATATAGCTTTCCCTCGAATAAATAATATAAGATTTTGACTTCTCCCCCCCTCTTTAATTTTATTAATTTCTAGAAGAATTGTAGAAACTGGGGCCGGAACAGGCTGAACAGTATACCCTCCTTTATCTTCAAATATTGCTCATGGGGGAGCTTCTGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCAATTAATTTTATTACAACTATTATTAATATACGAATTAGTAATATATCATTTGATCAAATACCTTTATTTGTTTGATCAGTAGGAATTACAGCTTTATTATTACTTTTATCTTTACCTGTATTAGCTGGAGCTATTACCATATTATTAACGGATCGAAATTTAAATACTTCATTTTTTGACCCTGCTGGAGGAGGAGATCCCATTCTTTATCAACATCTATTTTGATTTTTTGG'
expected = 'GNANNNNNNTTTTATTTTTGGNNNNNNNNN'
result = self.blast.strip_question_marks(seq)
self.assertTrue(result.startswith(expected))
seq = '?GGAAGAATTAGGTAACCCAGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACTGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAATTCCTTTAATACTTGGAGCTCCTGATATAGCTTTCCCTCGAATAAATAATATAAGATTTTGACTTCTCCCCCCCTCTTTAATTTTATTAATTTCTAGAAGAATTGTAGAAACTGGGGCCGGAACAGGCTGAACAGTATACCCTCCTTTATCTTCAAATATTGCTCATGGGGGAGCTTCTGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCAATTAATTTTATTACAACTATTATTAATATACGAATTAGTAATATATCATTTGATCAAATACCTTTATTTGTTTGATCAGTAGGAATTACAGCTTTATTATTACTTTTATCTTTACCTGTATTAGCTGGAGCTATTACCATATTATTAACGGATCGAAATTTAAATACTTCATTTTTTGACCCTGCTGGAGGAGGAGATCCCATTCTTTATCAACATCTATTTTGATTTTTTGG'
expected = 'GGAAGAATTAGGTAACCCAGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACTGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAATTCCTTTAATACTTGGAGCTCCTGATATAGCTTTCCCTCGAATAAATAATATAAGATTTTGACTTCTCCCCCCCTCTTTAATTTTATTAATTTCTAGAAGAATTGTAGAAACTGGGGCCGGAACAGGCTGAACAGTATACCCTCCTTTATCTTCAAATATTGCTCATGGGGGAGCTTCTGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCAATTAATTTTATTACAACTATTATTAATATACGAATTAGTAATATATCATTTGATCAAATACCTTTATTTGTTTGATCAGTAGGAATTACAGCTTTATTATTACTTTTATCTTTACCTGTATTAGCTGGAGCTATTACCATATTATTAACGGATCGAAATTTAAATACTTCATTTTTTGACCCTGCTGGAGGAGGAGATCCCATTCTTTATCAACATCTATTTTGATTTTTTGG'
result = self.blast.strip_question_marks(seq)
self.assertEqual(expected, result)