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Commit 7b801fe8 authored by Studer Gabriel's avatar Studer Gabriel
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make HHblits unit test specific to version 3, as version 2 is deprecated

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modules/bindings/tests/test_hhblits.py
+ 30
− 29
View file @ 7b801fe8
......@@ -12,7 +12,7 @@ import datetime
import ost
from ost import seq
from ost import settings
from ost.bindings import hhblits
from ost.bindings import hhblits3
class _UnitTestHHblitsLog(ost.LogSink):
"""Dedicated logger to hide some expected warning/ error messages.
......@@ -53,7 +53,7 @@ class TestHHblitsBindings(unittest.TestCase):
'PDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDV'+
'TGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYYYS'+
'KEAEAGNTKYAKVDGTKPVAEVRADLEKILG')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
# this works only as long as utils.TempDirWithFiles() names the first
# fasta file seq01.fasta
self.assertEqual(self.hh.filename[-11:], 'seq01.fasta')
......@@ -68,7 +68,7 @@ class TestHHblitsBindings(unittest.TestCase):
'TGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYYYS'+
'KEAEAGNTKYAKVDGTKPVAEVRADLEKILG')
tmpdir = tempfile.mkdtemp()
self.hh = hhblits.HHblits(query_seq, self.hhroot, working_dir=tmpdir)
self.hh = hhblits3.HHblits(query_seq, self.hhroot, working_dir=tmpdir)
self.assertEqual(self.hh.filename, os.path.join(tmpdir,
'query_hhblits.fasta'))
self.assertEqual(self.hh.working_dir, tmpdir)
......@@ -76,14 +76,14 @@ class TestHHblitsBindings(unittest.TestCase):
def testFileNoWDir(self):
# we have a sequence but no working dir
self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot)
self.hh = hhblits3.HHblits('testfiles/seq2.fasta', self.hhroot)
self.assertEqual(self.hh.filename[-10:], 'seq2.fasta')
def testFileWDir(self):
# we have a sequence and a working dir
tmpdir = tempfile.mkdtemp()
self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot,
working_dir=tmpdir)
self.hh = hhblits3.HHblits('testfiles/seq2.fasta', self.hhroot,
working_dir=tmpdir)
self.assertEqual(self.hh.filename, os.path.join(tmpdir, 'seq2.fasta'))
self.assertEqual(self.hh.working_dir, tmpdir)
self.hh.needs_cleanup = True
......@@ -91,8 +91,8 @@ class TestHHblitsBindings(unittest.TestCase):
def testDoCleanup(self):
# test that cleanup cleans up
tmpdir = tempfile.mkdtemp()
self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot,
working_dir=tmpdir)
self.hh = hhblits3.HHblits('testfiles/seq2.fasta', self.hhroot,
working_dir=tmpdir)
self.assertTrue(os.path.isdir(tmpdir))
self.hh.needs_cleanup = True
self.hh.Cleanup()
......@@ -101,8 +101,8 @@ class TestHHblitsBindings(unittest.TestCase):
def testDoNotCleanup(self):
# test that cleanup cleans up
tmpdir = tempfile.mkdtemp()
self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot,
working_dir=tmpdir)
self.hh = hhblits3.HHblits('testfiles/seq2.fasta', self.hhroot,
working_dir=tmpdir)
self.assertTrue(os.path.isdir(tmpdir))
self.hh.needs_cleanup = False
self.hh.Cleanup()
......@@ -113,8 +113,8 @@ class TestHHblitsBindings(unittest.TestCase):
def testCleanupFailed(self):
# test that cleanup cleans up
tmpdir = tempfile.mkdtemp()
self.hh = hhblits.HHblits('testfiles/seq2.fasta', self.hhroot,
working_dir=tmpdir)
self.hh = hhblits3.HHblits('testfiles/seq2.fasta', self.hhroot,
working_dir=tmpdir)
self.assertTrue(os.path.isdir(tmpdir))
self.hh.needs_cleanup = False
self.hh.CleanupFailed()
......@@ -123,7 +123,7 @@ class TestHHblitsBindings(unittest.TestCase):
def testFileNoExists(self):
# test on calling with a non-existing fasta file
with self.assertRaises(IOError) as ioe:
hhblits.HHblits('notthere.fasta', self.hhroot)
hhblits3.HHblits('notthere.fasta', self.hhroot)
self.assertEqual(ioe.exception.errno, 2)
self.assertEqual(ioe.exception.strerror, 'No such file or directory')
......@@ -134,7 +134,7 @@ class TestHHblitsBindings(unittest.TestCase):
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
a3m = self.hh.BuildQueryMSA('testfiles/hhblitsdb/unittestdb',
assign_ss = False)
self.assertTrue(filecmp.cmp(a3m, "testfiles/testali_two_no_ss.a3m"))
......@@ -146,7 +146,7 @@ class TestHHblitsBindings(unittest.TestCase):
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
_, self.tmpfile = tempfile.mkstemp(suffix='.hmm')
os.remove(self.tmpfile)
hhfile = self.hh.A3MToProfile("testfiles/testali.a3m",
......@@ -167,7 +167,7 @@ class TestHHblitsBindings(unittest.TestCase):
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
hhfile = self.hh.A3MToProfile("testfiles/testali.a3m")
with open(hhfile) as tfh:
tlst = tfh.readlines()
......@@ -186,7 +186,7 @@ class TestHHblitsBindings(unittest.TestCase):
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
hhfile = self.hh.A3MToProfile("testfiles/testali.a3m",
hhm_file="testfiles/test.hmm")
# when the hmm file already exists, its not touched, so files should be
......@@ -200,7 +200,7 @@ class TestHHblitsBindings(unittest.TestCase):
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
with self.assertRaises(IOError) as ioe:
self.hh.A3MToProfile("doesnotexist.a3m")
self.assertEqual(ioe.exception.errno, None)
......@@ -214,7 +214,7 @@ class TestHHblitsBindings(unittest.TestCase):
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
_, self.tmpfile = tempfile.mkstemp(suffix='.seq219')
os.remove(self.tmpfile)
csfile = self.hh.A3MToCS("testfiles/testali.a3m",
......@@ -231,7 +231,7 @@ class TestHHblitsBindings(unittest.TestCase):
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
csfile = self.hh.A3MToCS("testfiles/testali.a3m",
options={'-alphabet' :
......@@ -248,7 +248,7 @@ class TestHHblitsBindings(unittest.TestCase):
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
csfile = self.hh.A3MToCS("testfiles/testali.a3m",
cs_file='testfiles/test.seq219',
options={'-alphabet' :
......@@ -264,12 +264,12 @@ class TestHHblitsBindings(unittest.TestCase):
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
search_file = self.hh.Search("testfiles/testali.a3m",
'testfiles/hhblitsdb/unittestdb')
with open(search_file) as f:
header, hits = hhblits.ParseHHblitsOutput(f)
header, hits = hhblits3.ParseHHblitsOutput(f)
self.assertEqual(len(hits), 4)
exp_scores = [199.3, 12.3, 11.5, 8.1]
for hit_idx in range(4):
......@@ -281,14 +281,14 @@ class TestHHblitsBindings(unittest.TestCase):
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
with self.assertRaises(RuntimeError) as rte:
self.hh.Search("doesnotexist.a3m", 'testfiles/hhblitsdb/unittestdb')
def testParseHHMWorking(self):
# get info from an HHM file
with open("testfiles/test.hmm") as hhm_fh:
prof = hhblits.ParseHHM(hhm_fh)
prof = hhblits3.ParseHHM(hhm_fh)
self.assertEqual(''.join([str(x) for x in prof['ss_conf']]),
'999999999999998873391557999999998639441123987788888'+
'856788999999999998735477789999999887650299989899889'+
......@@ -307,7 +307,7 @@ class TestHHblitsBindings(unittest.TestCase):
# get info from an HHM file
with self.assertRaises(IOError) as ioe:
with open('testfiles/testali.a3m') as f:
hhblits.ParseHHM(f)
hhblits3.ParseHHM(f)
self.assertEqual(ioe.exception.args[0],
'Profile file "testfiles/testali.a3m" is missing '+
'the "Consensus" section')
......@@ -315,7 +315,7 @@ class TestHHblitsBindings(unittest.TestCase):
def testParseA3MWorking(self):
# get info from an HHM file
with open("testfiles/testali.a3m") as a3m_fh:
prof = hhblits.ParseA3M(a3m_fh)
prof = hhblits3.ParseA3M(a3m_fh)
self.assertEqual(''.join([str(x) for x in prof['ss_conf']]),
'999999999999998873391557999999998639441123987788888'+
'856788999999999998735477789999999887650299989899889'+
......@@ -329,7 +329,7 @@ class TestHHblitsBindings(unittest.TestCase):
def fastParseHeader(self):
header_line = ' 1 814cbc1899f35c872169524af30fc2 100.0 5E-100' + \
' 5E-104 710.5 34.1 277 3-293 2-280 (281)'
hit, offset = hhblits.ParseHeaderLine(header_line)
hit, offset = hhblits3.ParseHeaderLine(header_line)
self.assertEqual(hit.hit_id, '814cbc1899f35c872169524af30fc2')
self.assertAlmostEqual(hit.evalue, 0)
self.assertAlmostEqual(hit.prob, 100.0)
......@@ -339,7 +339,7 @@ class TestHHblitsBindings(unittest.TestCase):
def testParseHHblitsOutput(self):
with open("testfiles/test.hhr") as f:
header, hits = hhblits.ParseHHblitsOutput(f)
header, hits = hhblits3.ParseHHblitsOutput(f)
self.assertEqual(header.query, 'Test')
self.assertEqual(header.match_columns, 141)
self.assertEqual(header.n_eff, 9.4)
......@@ -420,6 +420,7 @@ class TestHHblitsBindings(unittest.TestCase):
if __name__ == "__main__":
try:
from ost.bindings import hhblits
hhblits_version_string = hhblits.GetHHblitsVersionString()
  • Gerardo Tauriello @taurielg ·
    Owner

    If the test is specific to HHblits 3 it might be good to explicitly check the version string to skip it if only version 2 is available...

  • Studer Gabriel @studga00 ·
    Author Maintainer

    Yes, that's the intended logic. See further down.

  • Gerardo Tauriello @taurielg ·
    Owner

    Oops. I thought I had checked the rest of the file but must have opened the wrong one. My bad. All good.

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except:
print("No HHblits installation found: skip unit tests")
......
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