def test_get_set_of_pbdid_from_pdb_seqres_txt_empty_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
open(task.get_pdb_seqres_txt(), 'a').close()
self.assertEqual(os.path.isfile(task.get_pdb_seqres_txt()), True)
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pbdid_from_pdb_seqres_txt_file_no_seqs(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
f = open(task.get_pdb_seqres_txt(), 'w')
f.write('hi\nhow\nare\nyou')
f.flush()
f.close()
self.assertEqual(os.path.isfile(task.get_pdb_seqres_txt()), True)
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres_w_hits(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
f = open(task.get_crystalph_tsv(), 'w')
f.write('PDB_ID _exptl_crystal_grow.pH\n')
f.write('4X09\t6.5\n')
f.write('4rfr\t8\n')
f.write('4XET\t6.2\n')
f.write('4XF1\t6.2\n')
f.write('4XF3\t6.2\n')
f.flush()
f.close()
makeblast = MakeBlastDBTask(temp_dir, params)
makeblast.create_dir()
f = open(makeblast.get_pdb_seqres_txt(), 'w')
f.write('>4rfr_A mol:protein length:154 MYOGLOBIN\n')
f.write('MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVK'
'HLKTEAEMKASEDLKKHG\n')
f.write('>102l_A mol:protein length:165 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKA'
'IGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAL'
'INMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRV'
'ITTFRTGTWDAYKNL\n')
f.flush()
f.close()
pdbset = task.get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres()
self.assertEqual(len(pdbset), 1)
self.assertEqual('4RFR' in pdbset, True)
finally:
shutil.rmtree(temp_dir)
def test_run_where_everything_is_successful(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = gzip.open(fakegz, 'wb')
f.write('hello\n')
f.flush()
f.close()
params.pdbsequrl = 'file://' + fakegz
params.makeblastdb = 'echo'
task = MakeBlastDBTask(temp_dir, params)
task._retrysleep = 0
task._maxretries = 1
task.run()
self.assertEqual(task.get_error(), None)
# check echo.stdout file for valid arguments
f = open(os.path.join(task.get_dir(), 'echo.stdout'), 'r')
line = f.readline()
self.assertEqual(
line, '-in ' + task.get_pdb_seqres_txt() + ' -out ' +
os.path.join(task.get_dir(), 'pdb_db') + ' -dbtype prot\n')
f.close()
lines = task.get_email_log().split('\n')
self.assertEqual(lines[2], '# sequence(s): 0')
f.close()
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pbdid_from_pdb_seqres_txt_with_400k_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
f = open(task.get_pdb_seqres_txt(), 'w')
perms = itertools.permutations(
string.ascii_lowercase + '123456789', 4)
counter = 0
try:
limit = 400000
while counter < limit:
f.write('>' + ''.join(map(str, perms.next())) +
'_A mol:protein length:165 T4 LYSOZYME\n')
f.write('MVLSEGEWQLVLH\n')
counter += 1
except StopIteration:
pass
f.flush()
f.close()
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), counter)
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pbdid_from_pdb_seqres_txt_with_seqs(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
f = open(task.get_pdb_seqres_txt(), 'w')
f.write('>101m_A mol:protein length:154 MYOGLOBIN\n')
f.write('MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVK'
'HLKTEAEMKASEDLKKHG\n')
f.write('>102l_A mol:protein length:165 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKA'
'IGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAL'
'INMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRV'
'ITTFRTGTWDAYKNL\n')
f.write('>102l_A mol:protein length:154 MYOGLOBIN\n')
f.write('MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHL'
'KTEAEMKASEDLKKAGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKI'
'PIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKELGYQG\n')
f.write('>103l_A mol:protein length:167 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNSLDAAKSELD'
'KAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRA'
'ALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAK'
'RVITTFRTGTWDAYKNL\n')
f.write('>10jj3m_A mol:protein length:154 MYOGLOBIN\n')
f.write('MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRF\n')
f.write('>104l_A mol:protein length:166 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSAAE\n')
f.write('>104l_B mol:protein length:166 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSAKNL\n')
f.flush()
f.close()
self.assertEqual(os.path.isfile(task.get_pdb_seqres_txt()), True)
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), 4)
self.assertEqual('101M' in pdbset, True)
self.assertEqual('102L' in pdbset, True)
self.assertEqual('103L' in pdbset, True)
self.assertEqual('104L' in pdbset, True)
finally:
shutil.rmtree(temp_dir)
def test_get_sequence_count_file_has_zero_size(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
open(task.get_pdb_seqres_txt(), 'a').close()
self.assertEqual(task._get_sequence_count_message(),
'# sequence(s): 0')
finally:
shutil.rmtree(temp_dir)
def get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres(self):
"""Gets set of PDBIDs that are in both tsv and sequence file
Examines `DataImportTask.CRYSTALPH_TSV` and
`MakeBlastDBTask.PDB_SEQRES_TXT` and returns a set of PDBIDs
that are in both files
:returns: set of PDBIDs uppercase that are in both files above
"""
make_blastdb = MakeBlastDBTask(self._path, self._args)
if not os.path.isfile(make_blastdb.get_pdb_seqres_txt()):
logger.warning('No ' + make_blastdb.get_pdb_seqres_txt() +
' file found')
return set()
c_pdbid_set = self.get_set_of_pdbid_from_crystalph_tsv()
if len(c_pdbid_set) == 0:
logger.warning('No PDBIds found in ' + self.get_crystalph_tsv())
return set()
seq_pdbid_set = make_blastdb.get_set_of_pbdid_from_pdb_seqres_txt()
if len(seq_pdbid_set) == 0:
logger.warning('No PDBIds found in ' +
make_blastdb.get_pdb_seqres_txt())
return set()
common_pdbid = set()
# iterate through tsv pdb ids and return any found in
# sequence pdb id set
for id in c_pdbid_set:
if id in seq_pdbid_set:
common_pdbid.add(id)
logger.debug('Found ' + str(len(common_pdbid)) + ' PDBIDs in ' +
self.get_crystalph_tsv() + ' and ' +
make_blastdb.get_pdb_seqres_txt())
return common_pdbid
def test_get_set_of_pbdid_from_pdb_seqres_txt_wrong_len_pdbids(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
f = open(task.get_pdb_seqres_txt(), 'w')
f.write('>1m_A mol:protein length:154 MYOGLOBIN\n')
f.write('MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVK'
'HLKTEAEMKASEDLKKHG\n')
f.write('>abcdel_A mol:protein length:165 T4 LYSOZYME\n')
f.write('MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKA'
'IGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAL'
'INMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRV'
'ITTFRTGTWDAYKNL\n')
f.flush()
f.close()
self.assertEqual(os.path.isfile(task.get_pdb_seqres_txt()), True)
pdbset = task.get_set_of_pbdid_from_pdb_seqres_txt()
self.assertEqual(len(pdbset), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_sequence_count_file_has_multiple_seqs(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = MakeBlastDBTask(temp_dir, params)
task.create_dir()
f = open(task.get_pdb_seqres_txt(), 'w')
f.write('>hi\n>seq\n>are\n')
f.flush()
f.close()
self.assertEqual(task._get_sequence_count_message(),
'# sequence(s): 3')
finally:
shutil.rmtree(temp_dir)
def test_run_where_gunzip_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = open(fakegz, 'w')
f.write('hello\n')
f.flush()
f.close()
params.pdbsequrl = 'file://' + fakegz
params.makeblastdb = 'makeblastdb'
task = MakeBlastDBTask(temp_dir, params)
task._retrysleep = 0
task._maxretries = 1
task.run()
self.assertEqual(
task.get_error(),
'Unable to uncompress file: ' + task.get_pdb_seqres_txt())
finally:
shutil.rmtree(temp_dir)
def test_get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres_empty_seq(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = DataImportTask(temp_dir, params)
task.create_dir()
f = open(task.get_crystalph_tsv(), 'w')
f.write('PDB_ID _exptl_crystal_grow.pH\n')
f.write('4X09\t6.5\n')
f.write('4rfr\t8\n')
f.write('4XET\t6.2\n')
f.write('4XF1\t6.2\n')
f.write('4XF3\t6.2\n')
f.flush()
f.close()
makeblast = MakeBlastDBTask(temp_dir, params)
makeblast.create_dir()
open(makeblast.get_pdb_seqres_txt(), 'a').close()
pdbset = task.get_set_of_pdbid_in_crystalph_tsv_and_pdb_seqres()
self.assertEqual(len(pdbset), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_pdbseqres_txt(self):
params = D3RParameters()
task = MakeBlastDBTask('/foo', params)
self.assertEqual(
task.get_pdb_seqres_txt(),
os.path.join('/foo', task.get_dir_name(), 'pdb_seqres.txt'))