def test_execute_script_its(self):
# Getting all ITS Sequences. Time: 963.44s
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta", "its"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was created.")
count = 0
idList = []
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
idList.append(line.split()[0])
self.assertEqual(23517, count,
"Expected 23517 sequences but got {}".format(count))
self.assertIn('>seqdb|131072', idList,
"Expected sequence ID 131072 is not found in the file")
self.assertIn('>seqdb|111872', idList,
"Expected sequence ID 11187 is not found in the file")
self.assertIn('>seqdb|131058', idList,
"Expected sequence ID 131071 is not found in the file")
def test_execute_script_raw_taxonomy(self):
# Filtering on Sample Name. Time: 3.40s
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta", "raw",
"-t", "--sampleName", "INVITRO221"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertTrue(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was not created.")
count = 0
idList = []
with open(self.output_taxon_file_name) as f:
for line in f:
count = count + 1
idList.append(line.split()[0])
self.assertEqual(6, count,
"Expected 6 sequences but got {}".format(count))
self.assertIn('961', idList,
"Expected taxonomy ID 961 is not the found in the file")
self.assertIn('97830', idList,
"Expected taxonomy ID 97830 is not found in the file")
self.assertIn('97847', idList,
"Expected taxonomy ID 97847 is not found in the file")
def test_execute_script_all_taxonomy(self):
# Filtering on Gene Region Name. Time: 124.98s
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta", "-t",
"all", "--geneRegion", "ACA"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertTrue(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
count = 0
idList = []
with open(self.output_taxon_file_name) as f:
for line in f:
count = count + 1
idList.append(line.split()[0])
self.assertEqual(1041, count,
"Expected 1,041 sequences but got {}".format(count))
self.assertIn('358301', idList,
"Expected taxonomy ID 358301 is not found in the file")
self.assertIn('37674', idList,
"Expected taxonomy ID 37674 is not found in the file")
self.assertIn('148710', idList,
"Expected taxonomy ID 148710 is not found in the file")
def test_execute_script_raw_fastq(self):
# Filtering on Sample Name. Time: 4.6s
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fastq", "raw",
"--sampleName", "LEV6103"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fastq_file_name),
"Fastq file was not created.")
self.assertFalse(os.path.isfile(self.output_fasta_file_name),
"Fasta file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was created.")
count = 0
idList = []
with open(self.output_fastq_file_name) as f:
for line in f:
if line.startswith('@'):
count = count + 1
idList.append(line.split()[0])
self.assertEqual(60, count,
"Expected 60 sequences but got {}".format(count))
self.assertIn('@seqdb|266400', idList,
"Expected sequence ID 266400 is not found in the file")
self.assertIn('@seqdb|301609', idList,
"Expected sequence ID 301609 is not found in the file")
self.assertIn('@seqdb|331086', idList,
"Expected sequence ID 331086 is not found in the file")
def test_execute_script_consensus_taxonomy(self):
# Filtering on Sequence Name. Time: 1.06s
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta", "-t",
"consensus", "--seqName", "Pyt_arrhenomanes_"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertTrue(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
count = 0
idList = []
with open(self.output_taxon_file_name) as f:
for line in f:
count = count + 1
idList.append(line.split()[0])
self.assertEqual(5, count,
"Expected 5 sequence but got {}".format(count))
self.assertIn('358301', idList,
"Expected taxonomy ID 358301 is not found in the file")
self.assertIn('358327', idList,
"Expected taxonomy ID 358327 is not found in the file")
self.assertIn('358485', idList,
"Expected taxonomy ID 358485 is not found in the file")
# Filtering on Taxonomy Rank and Taxonomy Value. Time: 2.49s
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta", "-t",
"consensus", "--taxRank", "species", "--taxValue", "megasperma"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertTrue(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
count = 0
idList = []
with open(self.output_taxon_file_name) as f:
for line in f:
count = count + 1
idList.append(line.split()[0])
self.assertEqual(3, count,
"Expected 3 sequence but got {}".format(count))
self.assertIn('358368', idList,
"Expected taxonomy ID 358301 is not found in the file")
self.assertIn('358385', idList,
"Expected taxonomy ID 358327 is not found in the file")
self.assertIn('358394', idList,
"Expected taxonomy ID 358485 is not found in the file")
def test_execute_script_consensus_fasta(self):
# Time: 86.143s
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta",
"consensus"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was created.")
count = 0
idList = []
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
idList.append(line.split()[0])
# Note that the number of all consensus sequences you get in SeqDB UI is 15037. This is a bug in
# SeqDB that there are some sequences that are not deleted properly, so they are reported as there,
# but they don't have any sequence information.
self.assertEqual(15037, count,
"Expected 15037 sequences but got {}".format(count))
self.assertIn('>seqdb|358301', idList,
"Expected sequence ID 358301 is not found in the file")
self.assertIn('>seqdb|4823203', idList,
"Expected sequence ID 4823203 is not found in the file")
self.assertIn('>seqdb|4829279', idList,
"Expected sequence ID 4829279 is not found in the file")
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta",
"consensus", "--geneRegion", "28s"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was created.")
count = 0
idList = []
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
idList.append(line.split()[0])
self.assertEqual(1499, count,
"Expected 1499 sequences but got {}".format(count))
self.assertIn('>seqdb|1582548', idList,
"Expected sequence ID 358301 is not found in the file")
self.assertIn('>seqdb|4825579', idList,
"Expected sequence ID 4823203 is not found in the file")
self.assertIn('>seqdb|4827758', idList,
"Expected sequence ID 4829279 is not found in the file")
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta",
"consensus", "--specNums", "4405,4264"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was created.")
count = 0
idList = []
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
idList.append(line.split()[0])
self.assertEqual(3, count,
"Expected 3 sequences but got {}".format(count))
self.assertIn('>seqdb|358301', idList,
"Expected sequence ID 358301 is not found in the file")
self.assertIn('>seqdb|358302', idList,
"Expected sequence ID 358301 is not found in the file")
self.assertIn('>seqdb|4825628', idList,
"Expected sequence ID 358301 is not found in the file")
def test_execute_script_all_fasta(self):
'''
#Getting All Sequences. Time: TOO LONG
pull_seqdb_seqs.execute_script(["-c", config_root.path() + '/config4tests.yaml', "-r", "fasta", "all"],
self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name), "Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name), "Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name), "Taxonomy file was created.")
count = 0
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
self.assertEqual(485643, count, "Expected 485,643 sequences but got {}".format(count))
'''
# Time: 32.8s
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta", "all",
"--geneRegion", "EF-1a"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was created.")
count = 0
idList = []
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
idList.append(line.split()[0])
self.assertEqual(492, count,
"Expected 492 sequences but got {}".format(count))
self.assertIn('>seqdb|1689', idList,
"Expected sequence ID 1689 is not found in the file")
self.assertIn('>seqdb|103372', idList,
"Expected sequence ID 103372 is not found in the file")
self.assertIn('>seqdb|149807', idList,
"Expected sequence ID 149807 is not found in the file")
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta", "all",
"--projectName", "Pythium Type Specimens"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was created.")
count = 0
idList = []
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
idList.append(line.split()[0])
self.assertEqual(4373, count,
"Expected 4,373 sequences but got {}".format(count))
self.assertIn('>seqdb|358305', idList,
"Expected sequence ID 1689 is not found in the file")
self.assertIn('>seqdb|196715', idList,
"Expected sequence ID 103372 is not found in the file")
self.assertIn('>seqdb|356858', idList,
"Expected sequence ID 149807 is not found in the file")
def test_execute_script_raw_fasta(self):
'''
#Getting all Raw Sequences. Time: TOO LONG
pull_seqdb_seqs.execute_script(["-c", config_root.path() + '/config4tests.yaml', "-r", "fasta", "raw"],
self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name), "Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name), "Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name), "Taxonomy file was created.")
count = 0
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
self.assertEqual(480088, count, "Expected 480,088 sequences but got {}".format(count))
'''
# Time: 10.5s
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta", "raw",
"--seqName", "S-SH-"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was created.")
count = 0
idList = []
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
idList.append(line.split()[0])
self.assertEqual(134, count,
"Expected 134 sequences but got {}".format(count))
self.assertIn('>seqdb|1', idList,
"Expected sequence ID 1 is not found in the file")
self.assertIn('>seqdb|79390', idList,
"Expected sequence ID 79390 is not found in the file")
self.assertIn('>seqdb|126059', idList,
"Expected sequence ID 126059 is not found in the file")
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta", "raw",
"--collectionCode", "pm"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was created.")
count = 0
idList = []
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
idList.append(line.split()[0])
self.assertEqual(148, count,
"Expected 148 sequences but got {}".format(count))
self.assertIn('>seqdb|268749', idList,
"Expected sequence ID 1 is not found in the file")
self.assertIn('>seqdb|308734', idList,
"Expected sequence ID 79390 is not found in the file")
self.assertIn('>seqdb|356572', idList,
"Expected sequence ID 126059 is not found in the file")
pull_seqdb_seqs.execute_script([
"-c",
config_root.path() + '/config4tests.yaml', "-r", "fasta", "raw",
"--specNums", "4405,4264"
], self.output_file_name, self.output_taxon_file_name)
self.assertTrue(os.path.isfile(self.output_fasta_file_name),
"Fasta file was not created.")
self.assertFalse(os.path.isfile(self.output_fastq_file_name),
"Fastq file was created.")
self.assertFalse(os.path.isfile(self.output_taxon_file_name),
"Taxonomy file was created.")
count = 0
idList = []
with open(self.output_fasta_file_name) as f:
for line in f:
if line.startswith('>'):
count = count + 1
idList.append(line.split()[0])
self.assertEqual(33, count,
"Expected 33 sequences but got {}".format(count))
self.assertIn('>seqdb|27755', idList,
"Expected sequence ID 358301 is not found in the file")
self.assertIn('>seqdb|155033', idList,
"Expected sequence ID 358301 is not found in the file")
self.assertIn('>seqdb|239733', idList,
"Expected sequence ID 358301 is not found in the file")