def test_blastnfilter_summary_parse_summary_file_on_validfile(self):
temp_dir = tempfile.mkdtemp()
try:
f = open(os.path.join(temp_dir, 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()
summary = BlastNFilterSummary(temp_dir)
self.assertEqual(summary.get_csv(), '0,0,178,95,71,67')
finally:
shutil.rmtree(temp_dir)
def test_blastnfilter_summary_parse_summary_file_on_dir(self):
temp_dir = tempfile.mkdtemp()
try:
os.mkdir(os.path.join(temp_dir, BlastNFilterTask.SUMMARY_TXT))
summary = BlastNFilterSummary(temp_dir)
self.assertEqual(summary.get_csv(), '0,0,0,0,0,0')
finally:
shutil.rmtree(temp_dir)
def test_blastnfilter_summary_week_and_year(self):
blast = BlastNFilterTask('/foo', D3RParameters())
summary = BlastNFilterSummary('/foo/2018/dataset.week.4'
'/' + blast.get_dir_name())
self.assertEqual(summary.get_week_number(), '4')
self.assertEqual(summary.get_year(), '2018')
self.assertEqual(summary.get_csv(), '4,2018,0,0,0,0')
def test_blastnfilter_summary_no_summary_file(self):
summary = BlastNFilterSummary('/foo')
self.assertEqual(summary.get_complexes(), 0)
self.assertEqual(summary.get_dockable_complexes(), 0)
self.assertEqual(summary.get_dockable_monomers(), 0)
self.assertEqual(summary.get_targets_found(), 0)
self.assertEqual(summary.get_week_number(), '0')
self.assertEqual(summary.get_year(), '0')
self.assertEqual(summary.get_csv(), '0,0,0,0,0,0')
def test_blastnfilter_summary_getters_and_setters(self):
summary = BlastNFilterSummary('/foo')
summary.set_complexes(5)
summary.set_dockable_complexes(6)
summary.set_dockable_monomers(7)
summary.set_targets_found(8)
self.assertEqual(summary.get_complexes(), 5)
self.assertEqual(summary.get_dockable_complexes(), 6)
self.assertEqual(summary.get_dockable_monomers(), 7)
self.assertEqual(summary.get_targets_found(), 8)
self.assertEqual(summary.get_csv(), '0,0,5,6,7,8')