def test_generate_reports_celppdir_does_not_exist(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = os.path.join(temp_dir, 'doesnotexist')
try:
celppreports.generate_reports(theargs)
self.assertEqual('Expected exception')
except Exception:
pass
finally:
shutil.rmtree(temp_dir)
def test_generate_reports_outdir_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
try:
celppreports.generate_reports(theargs)
self.assertEqual('Expected exception')
except Exception:
pass
finally:
shutil.rmtree(temp_dir)
def test_generate_reports_outdir_needs_to_be_created_no_celpp_data(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
outdir = os.path.join(temp_dir, 'outdir')
theargs.outdir = outdir
celppreports.generate_reports(theargs)
self.assertEqual(os.path.isdir(outdir), True)
csv_file = os.path.join(outdir, 'blastnfilter.summary.csv')
self.assertEqual(os.path.isfile(csv_file), True)
finally:
shutil.rmtree(temp_dir)
def test_generate_reports_with_one_week_in_one_year(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
outdir = os.path.join(temp_dir, 'outdir')
theargs.outdir = outdir
yeardir = os.path.join(temp_dir, '2016')
os.mkdir(yeardir)
weekdir = os.path.join(yeardir, 'dataset.week.10')
os.mkdir(weekdir)
blast = BlastNFilterTask(temp_dir, theargs)
blastdir = os.path.join(weekdir, blast.get_dir_name())
os.mkdir(blastdir)
# create dummary summary.txt file
f = open(os.path.join(blastdir, BlastNFilterTask.SUMMARY_TXT), 'w')
f.write('INPUT SUMMARY\n')
f.write(' entries: 221\n')
f.write(' complexes: 178\n')
f.write(' dockable complexes: 95\n')
f.write(' monomers: 145\n')
f.write(' dockable monomers: 71\n')
f.write(' multimers: 76\n')
f.write(' dockable multimers: 24\n\n')
f.write('FILTERING CRITERIA\n')
f.write(' No. of query sequences <= 1\n')
f.write(' No. of dockable ligands = 1\n')
f.write(' Percent identity >= 0.95\n')
f.write(' Percent Coverage >= 0.9\n')
f.write(' No. of hit sequences <= 4\n')
f.write(' Structure determination method: '
' x-ray diffraction\n\n')
f.write('OUTPUT SUMMARY\n')
f.write(' Targets found: 67\n')
f.write(' Target: 5fz7|Sequences: 1|Hits: 94|Candidates: 17|'
'Elected:4|PDBids: 5fz7,5fyz,5a3p,5a1f\n')
f.flush()
f.close()
celppreports.generate_reports(theargs)
self.assertEqual(os.path.isdir(outdir), True)
csv_file = os.path.join(outdir, 'blastnfilter.summary.csv')
self.assertEqual(os.path.isfile(csv_file), True)
# check csv file
f = open(csv_file, 'r')
header = f.readline()
self.assertEqual(
header, 'Week #, Year, Complexes, Dockable '
'complexes, Dockable monomers, '
'Targets Found\n')
data = f.readline()
self.assertEqual(data, '10,2016,178,95,71,67\n')
finally:
shutil.rmtree(temp_dir)