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''' Unit tests for the HHblits wrapper
'''
import unittest
import os
import sys
import tempfile
import shutil
import filecmp
import datetime
import ost
from ost import seq
from ost import settings
from ost import io
from ost.bindings import hhblits3
class _UnitTestHHblitsLog(ost.LogSink):
"""Dedicated logger to hide some expected warning/ error messages.
"""
def __init__(self):
ost.LogSink.__init__(self)
self.lcwd = os.getcwd()
def LogMessage(self, message, severity):
message = message.strip()
dnem = "could not open file '%s'" % os.path.join(self.lcwd,
'doesnotexist.a3m')
if message.endswith(dnem):
return
print(message)
def setUpModule():
ost.PushLogSink(_UnitTestHHblitsLog())
class TestHHblitsBindings(unittest.TestCase):
def setUp(self):
# expects default hhblits installation...
hhblits_bin_dir = os.path.dirname(settings.Locate('hhblits'))
self.hhroot = os.path.join(hhblits_bin_dir, os.pardir)
def tearDown(self):
if hasattr(self, 'hh'):
self.hh.Cleanup()
if hasattr(self, 'tmpfile'):
os.remove(self.tmpfile)
def testOSTSequenceNoWDir(self):
# OST sequence as input, no working dir should work
query_seq = seq.CreateSequence('1AKE.B',
'MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRA'+
'AVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQ'+
'EDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDV'+
'PDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDV'+
'TGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYYYS'+
'KEAEAGNTKYAKVDGTKPVAEVRADLEKILG')
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')
def testOSTSequenceWDir(self):
# OST sequence as input, with working dir should work
query_seq = seq.CreateSequence('1AKE.B',
'MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRA'+
'AVKSGSELGKQAKDIMDAGKLVTDELVIALVKERIAQ'+
'EDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDV'+
'PDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDV'+
'TGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYYYS'+
'KEAEAGNTKYAKVDGTKPVAEVRADLEKILG')
tmpdir = tempfile.mkdtemp()
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)
self.hh.needs_cleanup = True
def testFileNoWDir(self):
# we have a sequence but no working dir
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 = 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
def testDoCleanup(self):
# test that cleanup cleans up
tmpdir = tempfile.mkdtemp()
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()
self.assertFalse(os.path.isdir(tmpdir))
def testDoNotCleanup(self):
# test that cleanup cleans up
tmpdir = tempfile.mkdtemp()
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()
self.assertTrue(os.path.isdir(tmpdir))
shutil.rmtree(tmpdir)
self.assertFalse(os.path.isdir(tmpdir))
def testCleanupFailed(self):
# test that cleanup cleans up
tmpdir = tempfile.mkdtemp()
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()
self.assertFalse(os.path.isdir(tmpdir))
def testFileNoExists(self):
# test on calling with a non-existing fasta file
with self.assertRaises(IOError) as ioe:
hhblits3.HHblits('notthere.fasta', self.hhroot)
self.assertEqual(ioe.exception.errno, 2)
self.assertEqual(ioe.exception.strerror, 'No such file or directory')
def testProfile(self):
# try to create a search profile
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
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"))
def testA3mToProfileFileName(self):
# test A3mToProfile to work with a given hhmake_file name
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
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",
hhm_file=self.tmpfile)
with open(hhfile) as tfh:
tlst = tfh.readlines()
with open("testfiles/test.hmm") as efh:
elst = efh.readlines()
self.assertEqual(len(elst), len(tlst))
for i in range(0, len(elst)):
if elst[i].startswith("NULL"):
break # only compare header, profile is checked separately
if not elst[i].startswith(('FILE', 'COM', 'DATE')):
self.assertEqual(elst[i], tlst[i])
prof = io.LoadSequenceProfile(hhfile, format="hhm")
ref_prof = io.LoadSequenceProfile("testfiles/test.hmm", format="hhm")
hmm_transitions = [seq.HMMTransition.HMM_M2M, seq.HMMTransition.HMM_M2I,
seq.HMMTransition.HMM_M2D, seq.HMMTransition.HMM_I2M,
seq.HMMTransition.HMM_I2I, seq.HMMTransition.HMM_D2M,
seq.HMMTransition.HMM_D2D]
self.assertEqual(prof.sequence, ref_prof.sequence)
self.assertEqual(prof.neff, ref_prof.neff)
for col, ref_col in zip(prof.columns, ref_prof.columns):
hmm_data = col.hmm_data
ref_hmm_data = ref_col.hmm_data
self.assertAlmostEqual(hmm_data.neff, ref_hmm_data.neff, places=2)
self.assertAlmostEqual(hmm_data.neff_i, ref_hmm_data.neff_i,
places=2)
self.assertAlmostEqual(hmm_data.neff_d, ref_hmm_data.neff_d,
places=2)
for t in hmm_transitions:
self.assertAlmostEqual(hmm_data.GetProb(t),
ref_hmm_data.GetProb(t), places=2)
for olc in "ARNDQEKSCMWYTVILGPHF":
self.assertAlmostEqual(col.GetFreq(olc), ref_col.GetFreq(olc),
places=2)
def testA3mToProfileWithoutFileName(self):
# test A3mToProfile to work without a given hhmake_file name
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
hhfile = self.hh.A3MToProfile("testfiles/testali.a3m")
with open(hhfile) as tfh:
tlst = tfh.readlines()
with open("testfiles/test.hmm") as efh:
elst = efh.readlines()
self.assertEqual(len(elst), len(tlst))
for i in range(0, len(elst)):
if elst[i].startswith("NULL"):
break # only compare header, profile is checked separately
if not elst[i].startswith(('FILE', 'COM', 'DATE')):
self.assertEqual(elst[i], tlst[i])
prof = io.LoadSequenceProfile(hhfile, format="hhm")
ref_prof = io.LoadSequenceProfile("testfiles/test.hmm", format="hhm")
hmm_transitions = [seq.HMMTransition.HMM_M2M, seq.HMMTransition.HMM_M2I,
seq.HMMTransition.HMM_M2D, seq.HMMTransition.HMM_I2M,
seq.HMMTransition.HMM_I2I, seq.HMMTransition.HMM_D2M,
seq.HMMTransition.HMM_D2D]
self.assertEqual(prof.sequence, ref_prof.sequence)
self.assertEqual(prof.neff, ref_prof.neff)
for col, ref_col in zip(prof.columns, ref_prof.columns):
hmm_data = col.hmm_data
ref_hmm_data = ref_col.hmm_data
self.assertAlmostEqual(hmm_data.neff, ref_hmm_data.neff, places=2)
self.assertAlmostEqual(hmm_data.neff_i, ref_hmm_data.neff_i,
places=2)
self.assertAlmostEqual(hmm_data.neff_d, ref_hmm_data.neff_d,
places=2)
for t in hmm_transitions:
self.assertAlmostEqual(hmm_data.GetProb(t),
ref_hmm_data.GetProb(t), places=2)
for olc in "ARNDQEKSCMWYTVILGPHF":
self.assertAlmostEqual(col.GetFreq(olc), ref_col.GetFreq(olc),
places=2)
os.remove(hhfile)
def testA3mToProfileWithExistingFile(self):
# test A3mToProfile to work with an existing hmm file
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
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
# completely equal.
self.assertTrue(filecmp.cmp(hhfile, "testfiles/test.hmm"))
def testA3mToProfileWithoutA3m(self):
# test A3mToProfile to fail if we do not have an a3m file.
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
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)
self.assertEqual(ioe.exception.args[0],
"could not convert a3m to hhm file")
def testA3mToCSFileName(self):
# test A3mToCS to work with a given hhmake_file name
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
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",
cs_file=self.tmpfile, options={'-alphabet' :
os.path.join(self.hhroot,
'data',
'cs219.lib')})
self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219'))
def testA3mToCSNoFileName(self):
# test A3mToCS to work with a given hhmake_file name
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
csfile = self.hh.A3MToCS("testfiles/testali.a3m",
options={'-alphabet' :
os.path.join(self.hhroot,
'data',
'cs219.lib')})
self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219'))
self.tmpfile = "testfiles/testali.seq219"
def testA3mToCSFileExists(self):
# test A3mToCS to work with a given hhmake_file name
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
self.hh = hhblits3.HHblits(query_seq, self.hhroot)
csfile = self.hh.A3MToCS("testfiles/testali.a3m",
cs_file='testfiles/test.seq219',
options={'-alphabet' :
os.path.join(self.hhroot,
'data',
'cs219.lib')})
self.assertTrue(filecmp.cmp(csfile, 'testfiles/test.seq219'))
def testSearchWorking(self):
# successful search
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
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 = hhblits3.ParseHHblitsOutput(f)
self.assertEqual(len(hits), 4)
exp_scores = [199.3, 12.3, 11.5, 8.1]
for hit_idx in range(4):
self.assertAlmostEqual(hits[hit_idx].score, exp_scores[hit_idx])
def testSearchNotWorking(self):
query_seq = seq.CreateSequence('Test', 'VLSPADKTNVKAAWGKVGAHAGEYGAEA'+
'LERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVAD'+
'ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL'+
'LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVL'+
'TSKYR')
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 = hhblits3.ParseHHM(hhm_fh)
self.assertEqual(''.join([str(x) for x in prof['ss_conf']]),
'999999999999998873391557999999998639441123987788888'+
'856788999999999998735477789999999887650299989899889'+
'999999997536679989999999999999999984329')
self.assertEqual(''.join(prof['ss_pred']), 'CCCHHHHHHHHHHHHHHHCCCHHHH'+
'HHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCH'+
'HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH'+
'HHHHHHHHHHHHCC')
self.assertEqual(str(prof['consensus']), 'xltxxxxxxixxsWxxvxxxxxxxgxx'+
'xxxxlfxxxPxxxxxFxxxxxxxxxxxxxxhxxxvxxxlxxxixxldxxxx'+
'xlxxlxxxHxxxxgvxxxxxxxxxxxlxxxlxxxxgxxxxxxxxxAWxxxx'+
'xxixxxmxxxyx')
self.assertEqual(prof['msa'].GetCount(), 7)
def testParseHHMNotWorking(self):
# get info from an HHM file
with self.assertRaises(IOError) as ioe:
with open('testfiles/testali.a3m') as f:
hhblits3.ParseHHM(f)
self.assertEqual(ioe.exception.args[0],
'Profile file "testfiles/testali.a3m" is missing '+
'the "Consensus" section')
def testParseA3MWorking(self):
# get info from an HHM file
with open("testfiles/testali.a3m") as a3m_fh:
prof = hhblits3.ParseA3M(a3m_fh)
self.assertEqual(''.join([str(x) for x in prof['ss_conf']]),
'999999999999998873391557999999998639441123987788888'+
'856788999999999998735477789999999887650299989899889'+
'999999997536679989999999999999999984329')
self.assertEqual(''.join(prof['ss_pred']), 'CCCHHHHHHHHHHHHHHHCCCHHHH'+
'HHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCH'+
'HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH'+
'HHHHHHHHHHHHCC')
self.assertEqual(prof['msa'].GetCount(), 253)
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 = hhblits3.ParseHeaderLine(header_line)
self.assertEqual(hit.hit_id, '814cbc1899f35c872169524af30fc2')
self.assertAlmostEqual(hit.evalue, 0)
self.assertAlmostEqual(hit.prob, 100.0)
self.assertAlmostEqual(hit.pvalue, 0)
self.assertAlmostEqual(hit.score, 710.5)
self.assertAlmostEqual(hit.ss_score, 34.1)
def testParseHHblitsOutput(self):
with open("testfiles/test.hhr") as f:
header, hits = hhblits3.ParseHHblitsOutput(f)
self.assertEqual(header.query, 'Test')
self.assertEqual(header.match_columns, 141)
self.assertEqual(header.n_eff, 9.4)
self.assertEqual(header.searched_hmms, 5)
self.assertEqual(header.date,
datetime.datetime.strptime('Mon Aug 31 16:45:45 2015',
'%a %b %d %H:%M:%S %Y'))
self.assertEqual(header.command, '/import/bc2/apps/HH-suite/2.0.16-go'+
'olf-1.4.10/bin/hhblits -cpu 1 -n 1 -e 0.001 -Z 1000'+
'0 -B 10000 -i /import/bc2/home/schwede/bienert/git/'+
'ost_newenv.git/modules/bindings/tests/testfiles/tes'+
'tali.a3m -o /scratch/tmp9E5dor/testali_cpu1_n1.hhr '+
'-d /import/bc2/home/schwede/bienert/git/ost_newenv.'+
'git/modules/bindings/tests/testfiles/hhblitsdb/hhbl'+
'itsdb')
self.assertEqual(len(hits), 4)
# hit 1
self.assertEqual(hits[0].hit_id, '3e7b90809bd446a538f9eb1a1ca0e551')
self.assertEqual(hits[0].score, float('222.3'))
self.assertEqual(hits[0].ss_score, float('16.4'))
self.assertEqual(hits[0].evalue, float('2.7e-42'))
self.assertEqual(hits[0].pvalue, float('6.9E-45'))
self.assertEqual(hits[0].prob, float('100.0'))
self.assertEqual(str(hits[0].aln),
'Test VLSPADKTNVKAAWGKVGAHAGEYGAEALER'+
'MFLSFPTTKTYFPHF-DL-S----HGSAQ\n3e7b90809bd446a5... '+
'VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKT'+
'EAEMKASED\n\nTest VKGHGKKVADALTNAVAH'+
'VDDMPNALSALSDLHAHK-LRVDPVNFKLLSHCLLVTLAAHL\n3e7b908'+
'09bd446a5... LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHA-TKH'+
'KIPIKYLEFISEAIIHVLHSRH\n\nTest PAEFT'+
'PAVHASLDKFLASVSTVLTSKYR\n3e7b90809bd446a5... PGDFGA'+
'DAQGAMNKALELFRKDIAAKYK\n')
# hit 2
self.assertEqual(hits[1].hit_id, 'af828e69a5f2d0fd42a2a213e09eb64f')
self.assertEqual(hits[1].score, float('215.7'))
self.assertEqual(hits[1].ss_score, float('17.2'))
self.assertEqual(hits[1].evalue, float('1.5e-41'))
self.assertEqual(hits[1].pvalue, float('3.9E-44'))
self.assertEqual(hits[1].prob, float('100.0'))
self.assertEqual(str(hits[1].aln),
'Test VLSPADKTNVKAAWGKVGAHAGEYGAEALER'+
'MFLSFPTTKTYFPHFDLSHGSAQVKGHGK\naf828e69a5f2d0fd... '+
'VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHG'+
'SAQVKGHGK\n\nTest KVADALTNAVAHVDDMPN'+
'ALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA\naf828e6'+
'9a5f2d0fd... KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNF'+
'KLLSHCLLVTLAAHLPAEFTPA\n\nTest VHASL'+
'DKFLASVSTVLTSKYR\naf828e69a5f2d0fd... VHASLDKFLASVS'+
'TVLTSKYR\n')
# hit 3
self.assertEqual(hits[2].hit_id, '9287755aa6aa27583da6be3b2408bfcc')
self.assertEqual(hits[2].score, float('215.1'))
self.assertEqual(hits[2].ss_score, float('16.5'))
self.assertEqual(hits[2].evalue, float('3.8e-41'))
self.assertEqual(hits[2].pvalue, float('9.7E-44'))
self.assertEqual(hits[2].prob, float('100.0'))
self.assertEqual(str(hits[2].aln),
'Test VLSPADKTNVKAAWGKVGAHAGEYGAEALER'+
'MFLSFPTTKTYFPHF-DLS-----HGSAQ\n9287755aa6aa2758... '+
'HLTPEEKSAVTALWGKVN--VDEVGGEALGRLLVVYPWTQRFFESFGDLST'+
'PDAVMGNPK\n\nTest VKGHGKKVADALTNAVAH'+
'VDDMPNALSALSDLHAHK-LRVDPVNFKLLSHCLLVTLAAHL\n9287755'+
'aa6aa2758... VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHC-DKL'+
'HVDPENFRLLGNVLVCVLAHHF\n\nTest PAEFT'+
'PAVHASLDKFLASVSTVLTSKYR\n9287755aa6aa2758... GKEFTP'+
'PVQAAYQKVVAGVANALAHKYH\n')
# hit 4
self.assertEqual(hits[3].hit_id, 'e69e1ac0a4b2554df25f2c2183b0fba0')
self.assertEqual(hits[3].score, float('12.6'))
self.assertEqual(hits[3].ss_score, float('2.6'))
self.assertEqual(hits[3].evalue, float('64.0'))
self.assertEqual(hits[3].pvalue, float('0.16'))
self.assertEqual(hits[3].prob, float('0.6'))
self.assertEqual(str(hits[3].aln),
'Test VDPVNFKLLSHCLLVTLAAHL\ne69e1ac0'+
'a4b2554d... ATPEQAQLVHKEIRKIVKDTC\n')
if __name__ == "__main__":
try:
from ost.bindings import hhblits
hhblits_version_string = hhblits.GetHHblitsVersionString()
except:
print("No HHblits installation found: skip unit tests")
sys.exit(0)
if hhblits_version_string is None:
print("Could not identify HHblits version: skip unit tests")
sys.exit(0)
hhblits_version_major = int(hhblits_version_string.split('.')[0])
if hhblits_version_major != 3:
print("Found hhblits with major version %i. Unit tests only run with "\
"version 3: skip unit tests"%(hhblits_version_major))
sys.exit(0)
from ost import testutils
testutils.RunTests()
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