def test_outdir(self):
outdir = tempfile.mkdtemp(prefix='splitseq_')
mask_sequence(self.file_missed,
self.file_query,
outdir,
max_evalue=0.1,
min_fragment_length=40)
exp_filecontents = {
'non_match':
[('>NZ_GG666849.1_2_251-330 # 798 # 2885 # -1 # ID=1_2;parti'
'al=00;start_type=TTG;rbs_motif=AGxAGG/AGGxGG;rbs_spacer=5-10bp'
';gc_cont=0.499\n'),
('IGIQGDTYSEDEDYPELPRTANGRLSSYILVNHKEQVHVYNQIATKLGLQKESGEVVMLPSQ'
'FINRFSLRNEHGRGIPDQ\n')],
'match': []
}
obs_filecontents = dict()
for type_ in ('match', 'non_match'):
filename = outdir + '.' + type_
f = open(filename, 'r')
obs_filecontents[type_] = f.readlines()
f.close()
os.remove(filename)
shutil.rmtree(outdir)
self.assertDictEqual(obs_filecontents, exp_filecontents)
def test_outdir(self):
outdir = tempfile.mkdtemp(prefix='splitseq_')
mask_sequence(self.file_missed,
self.file_query,
outdir,
max_evalue=0.1,
min_fragment_length=40)
exp_filecontents = {
'non_match':
[('>NZ_GG666849.1_2_251-330 # 798 # 2885 # -1 # ID=1_2;parti'
'al=00;start_type=TTG;rbs_motif=AGxAGG/AGGxGG;rbs_spacer=5-10bp'
';gc_cont=0.499\n'),
('IGIQGDTYSEDEDYPELPRTANGRLSSYILVNHKEQVHVYNQIATKLGLQKESGEVVMLPSQ'
'FINRFSLRNEHGRGIPDQ\n')],
'match': []}
obs_filecontents = dict()
for type_ in ('match', 'non_match'):
filename = outdir+'.'+type_
f = open(filename, 'r')
obs_filecontents[type_] = f.readlines()
f.close()
os.remove(filename)
shutil.rmtree(outdir)
self.assertDictEqual(obs_filecontents, exp_filecontents)
def test_split_search_parseerror_2(self):
mask_sequence(self.file_hhsearch2,
self.file_fasta2,
min_prob=95.0,
min_fragment_length=40)
parse_pdb_match(self.file_hhsearch2)
def test_split_search_parseerror_2(self):
mask_sequence(self.file_hhsearch2,
self.file_fasta2,
min_prob=95.0,
min_fragment_length=40)
parse_pdb_match(self.file_hhsearch2)
def test_mask_sequence(self):
obs_res = mask_sequence(self.file_missed,
self.file_query,
None,
max_evalue=0.1,
min_fragment_length=40)
# check that hit selection works correct
self.assertEqual(obs_res, self.exp_hits)
def test_mask_sequence(self):
obs_res = mask_sequence(self.file_missed,
self.file_query,
None,
max_evalue=0.1,
min_fragment_length=40)
# check that hit selection works correct
self.assertEqual(obs_res, self.exp_hits)
def test_level2(self):
obs = mask_sequence(self.file_out2, self.file_fasta2, max_evalue=0.1,
min_fragment_length=40)
positions = []
for type_ in sorted(obs.keys()):
for header in sorted(obs[type_]):
start, stop = \
header[0].split(' # ')[0].split('_')[-1].split('-')
positions.append((type_, start, stop))
self.assertEqual(positions, self.pos2)
def test_pretty_output(self):
pretty_fp = get_data_path('test_split_search/NC_000913.3_2.pretty')
with open(pretty_fp, 'r') as f:
pretty = f.read()
mask_obs = mask_sequence(self.file_a,
self.file_query,
min_fragment_length=5)
with captured_output() as (out, err):
pretty_output(mask_obs)
output = out.getvalue()
self.maxDiff = None
self.assertEqual(output, pretty)
def test_mask_sequence_information(self):
seq = ('MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALP'
'NISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALIC'
'RGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVL'
'MAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKS'
'MSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGIS'
'NLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAER'
'AMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGS'
'SERSISVVVNNDDATTGVRVTHQMLFN')
header = ('gi|556503834|ref|NC_000913.3|_2_1-461 # 2j0w_A # 337 # 2799'
' # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG'
';rbs_spacer=5-10bp;gc_cont=0.531')
exp = (header, seq)
obs = mask_sequence(self.file_a,
self.file_query,
min_fragment_length=450)
self.assertEqual(obs['match'][0], exp)
filename = '/tmp/test.mfa'
mask_sequence(self.file_a,
self.file_query,
filename,
min_fragment_length=450)
f = open(filename + '.match', 'r')
obs = f.readlines()
f.close()
os.remove(filename + '.match')
self.assertIn(seq + "\n", obs)
self.assertIn(">" + header + "\n", obs)
f = open(filename + '.non_match', 'r')
obs = f.readlines()
f.close()
os.remove(filename + '.non_match')
self.assertFalse(obs)
with self.assertRaises(IOError):
mask_sequence(self.file_a, self.file_query, '/dev')
def test_mask_sequence(self):
match_header_2 = (
'gi|556503834|ref|NC_000913.3|_2_464-815 # 1ebf_A # 337 # 2799 # '
'1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spa'
'cer=5-10bp;gc_cont=0.531')
# test default behaviour
obs = mask_sequence(self.fp_out, self.fp_seqs)
self.assertEqual([m[0] for m in obs['match']], [
('gi|556503834|ref|NC_000913.3|_2_1-461 # 2j0w_A # 337 # 2799 # 1 '
'# ID=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_space'
'r=5-10bp;gc_cont=0.531'), match_header_2
])
# restrict hits to satisfy at least 33% sequence identifty
# --> first match will differ from default above
obs = mask_sequence(self.fp_out, self.fp_seqs, min_identity=0.33)
self.assertEqual([m[0] for m in obs['match']], [
('gi|556503834|ref|NC_000913.3|_2_1-462 # 3c1m_A # 337 # 2799 # 1 '
'# ID=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_space'
'r=5-10bp;gc_cont=0.531'), match_header_2
])
def test_level2(self):
obs = mask_sequence(self.file_out2,
self.file_fasta2,
max_evalue=0.1,
min_fragment_length=40)
positions = []
for type_ in sorted(obs.keys()):
for header in sorted(obs[type_]):
start, stop = \
header[0].split(' # ')[0].split('_')[-1].split('-')
positions.append((type_, start, stop))
self.assertEqual(positions, self.pos2)
def test_mask_sequence(self):
obs = mask_sequence(self.fp_out,
self.fp_seqs,
subsequences_fp='kurt_',
min_prob=95.0,
max_evalue=0.1,
min_fragment_length=40)
self.assertEqual(
obs['match'][0][1],
('TMEELLTSLQKKCGTECEEAHRQLVCALNGLAGIHIIKGEYALAAELYREVLRSSEEHKGKLK'
'TDSLQRLHATHNLMELLIARHPGIPPTLRDGRLEEEAKQLREHYMSKCNTEVAEAQQALYPVQ'
'QTIHELQRKIHSNSPWWLNVIHRAIEFTIDEELVQRVRNEITSNYKQQTGKLSMSEKFRDCRG'
'LQFLLTTQMEELNKCQKLVREAVKNLEGPPSRNVIESATVCHLRPARLPLNCCVFCKADELFT'
'EYESKLFSNTVKGQTAIFEEMIEDEEGLVDDRAPTTTRGLWAISETERSMKAILSFAKSHRFD'
'VEFVDEGSTSMDLFEAWKKEYKLLHEYWMALRNRVSAVDELAMATERLRVRDPREPKPNPPVL'
'HIIEPHEVEQNRIKLLNDKAVATSQLQKKLGQLLYLTNLEK'))
exp_0 = {
'Probab':
100.0,
'Template_Neff':
8.5,
'P-value':
2.8e-85,
'Similarity':
1.445,
'Sum_probs':
363.5,
'Score':
555.49,
'Cols':
419,
'No':
1,
'Identities':
1.0,
'SS':
0.0,
'alignment': {
'Q T0831': {
'start':
1,
'end':
419,
'sequence':
('TMEELLTSLQKKCGTECEEAHRQLVCALNGLAGIHIIKGEYALAAELYREVLRSSE'
'EHKGKLKTDSLQRLHATHNLMELLIARHPGIPPTLRDGRLEEEAKQLREHYMSKCN'
'TEVAEAQQALYPVQQTIHELQRKIHSNSPWWLNVIHRAIEFTIDEELVQRVRNEIT'
'SNYKQQTGKLSMSEKFRDCRGLQFLLTTQMEELNKCQKLVREAVKNLEGPPSRNVI'
'ESATVCHLRPARLPLNCCVFCKADELFTEYESKLFSNTVKGQTAIFEEMIEDEEGL'
'VDDRAPTTTRGLWAISETERSMKAILSFAKSHRFDVEFVDEGSTSMDLFEAWKKEY'
'KLLHEYWMALRNRVSAVDELAMATERLRVRDPREPKPNPPVLHIIEPHEVEQNRIK'
'LLNDKAVATSQLQKKLGQLLYLTNLEK'),
'totallen':
419
},
'Q Consensus': {
'start':
1,
'end':
419,
'sequence':
('tmeelltslqkkcgteceeahrqlvcalnglagihiikgeyalaaelyrevlrsse'
'ehkgklktdslqrlhathnlmelliarhpgipptlrdgrleeeakqlrehymskcn'
'tevaeaqqalypvqqtihelqrkihsnspwwlnvihraieftideelvqrvrneit'
'snykqqtgklsmsekfrdcrglqfllttqmeelnkcqklvreavknlegppsrnvi'
'esatvchlrparlplnccvfckadelfteyesklfsntvkgqtaifeemiedeegl'
'vddraptttrglwaisetersmkailsfakshrfdvefvdegstsmdlfeawkkey'
'kllheywmalrnrvsavdelamaterlrvrdprepkpnppvlhiiepheveqnrik'
'llndkavatsqlqkklgqllyltnlek'),
'totallen':
419
},
'column score': {
'sequence':
('||+|++..|-++|-+|||+++|++|.++|||||||||+|+|..|+++||+||+..+'
'++++++++|+||++|+.|||.+++...+||+||+++|..+.+++.+++..|++++.'
'..+..|++.+.++.+.+++++.+.++.++||+.+++.+++..++..++++|+++++'
'.+|.+..|..++..+|++.+||.+.+++.+++|.++.+-+.+++++|++||..+++'
'+++..||++|.+-+...|.+|++++.|..||+.||+.+.+|.+..+++++++++|.'
'.++.....++|.|+.|+.|+.+|.|++|++++.|+.+++.+|..-++++++|||||'
'+.++.+|++.+..++|.|||.|++-|+|.++|.++.|+||..++|.|+++++.+.+'
'+.+++.++...|++++|||.||.||.|')
},
'T Consensus': {
'start':
2,
'end':
420,
'sequence':
('tmeell~~Li~k~~~eceea~R~~v~~~NgLAgl~~l~~~~~~A~~~YrevL~~~~'
'~~~~~~~~D~Lq~iH~l~NL~~~l~~~~~~~~~~~~~~~l~~~~~~l~~~Yl~~~~'
'~~~~~a~~~~~~~~~~~~~~~~~~~~~~~Ww~~~l~~~~~~~~~~~l~~~i~~~l~'
'~~~~~~~~~~~~~~~~~s~~gL~~~l~~~l~~L~~~R~~l~~~l~~L~~~~~~~~v'
'~~~~~Ch~~~~~~~~~~C~~C~~~~~~~~yE~~Lf~~~~~~~~~~~~~~~~~~~~~'
'~~~~~~~~~~g~~~~S~~e~~lk~i~~~~r~~~~~~~~~~~~~~hl~~le~~rkEf'
'~~~r~lw~~~~~~l~a~DEL~ma~~Rlrl~~~~e~~~~~~~~~~i~~~ev~~~~~~'
'~~~e~~~a~~~l~r~~gqLrYL~nL~k'),
'totallen':
420
},
'T 4QN1_A': {
'start':
2,
'end':
420,
'sequence':
('TMEELLTSLQKKCGTECEEAHRQLVCALNGLAGIHIIKGEYALAAELYREVLRSSE'
'EHKGKLKTDSLQRLHATHNLMELLIARHPGIPPTLRDGRLEEEAKQLREHYMSKCN'
'TEVAEAQQALYPVQQTIHELQRKIHSNSPWWLNVIHRAIEFTIDEELVQRVRNEIT'
'SNYKQQTGKLSMSEKFRDCRGLQFLLTTQMEELNKCQKLVREAVKNLEGPPSRNVI'
'ESATVCHLRPARLPLNCCVFCKADELFTEYESKLFSNTVKGQTAIFEEMIEDEEGL'
'VDDRAPTTTRGLWAISETERSMKAILSFAKSHRFDVEFVDEGSTSMDLFEAWKKEY'
'KLLHEYWMALRNRVSAVDELAMATERLRVRDPREPKPNPPVLHIIEPHEVEQNRIK'
'LLNDKAVATSQLQKKLGQLLYLTNLEK'),
'totallen':
420
},
'T ss_dssp': {
'sequence':
('HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHH'
'HTTTTCCCCHHHHHHHHHHHHHCCCCCTTSSCCCTTTTTHHHHHHHHHHHHHHHHH'
'HHHHHHHHTTHHHHHHHHHHHHSSCSSSCHHHHHHHHHHHTTCHHHHHHHHHHHHC'
'CC----------GGGCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHH'
'HHHCCCCCSCSSSCCCCSHHHHHHHHHHHHHHHHBCCC------------------'
'-----------CCSBCHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH'
'HHHHHHHHHHHHHHHHHHHHHHHHCCCEECCC---------CCEECTTCHHHHHHH'
'HHHHHHHHHHHHHHHHHHHHHHHTTCC')
},
'T ss_pred': {
'sequence':
('CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH'
'HhhcCCccchHHHHHHHhhHHHHHHhcCCCCCCCcchhHHHHHHHHHHHHHHHHHH'
'HHHHHHHHHHHHHHHHHHHHHHhhccCCcHHHHHHHHHHHCCCcHHHHHHHHHHHH'
'hhcccccCCcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHH'
'HHhhcCCCCCCCCCCCCCCccccHHHHHHHHHHHhhcccCCCccchHhhhhccccc'
'cccCCCcccCCcccccHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHH'
'HHHHHHHHHHHHHHHHHHHHHHchhhheeCCCCCCCCCCCcccccCHHHHHHHHHH'
'HHHHHHHHHHHHHHHHHHHHHHhcccC')
},
'Confidence': {
'sequence':
('79999999999999999999999999999999999999999999999999999999'
'99999999999999999999999999999999999999999999999999999999'
'99999999999999999999988888999999999998877899999999999999'
'99987777778999999999999999999999999999999999999999999999'
'99999999999877789999999999999999999999999999999999999999'
'99888889999999999999999999999999999999999999999999999999'
'99999999999999999999999999999999999999999999999999999999'
'999999999999999999999999976')
},
},
'Aligned_cols':
419,
'E-value':
1.6e-80,
'Hit': ('4QN1_A E3 ubiquitin-protein ligase SHPRH; SHPRH, E3 ligas'
'e, RING, Ubiquitin; 2.48A {H**o sapiens}')
}
obs = parse_pdb_match(self.fp_out)
for k in obs[0].keys():
if type(obs[0][k]) == dict():
self.assertCountEqual(obs[0][k], exp_0[k])
else:
self.assertEqual(obs[0][k], exp_0[k])
with open(get_data_path('test_split_search/T0831_block0.out'),
'r') as f:
block = "".join(f.readlines())
obs = _parse_hit_block(block)
for k in obs.keys():
if type(obs[k]) == dict():
self.assertCountEqual(obs[k], exp_0[k])
else:
self.assertEqual(obs[k], exp_0[k])
def test_mask_sequence_filtering(self):
s1 = (('gi|556503834|ref|NC_000913.3|_2_1-461 # 2j0w_A # 337 # 2799 # '
'1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_s'
'pacer=5-10bp;gc_cont=0.531'),
('MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALP'
'NISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALIC'
'RGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVL'
'MAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKS'
'MSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGIS'
'NLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAER'
'AMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGS'
'SERSISVVVNNDDATTGVRVTHQMLFN'))
s2 = (('gi|556503834|ref|NC_000913.3|_2_462-463 # 337 # 2799 # 1 # ID='
'1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer='
'5-10bp;gc_cont=0.531'), 'TD')
s3 = (('gi|556503834|ref|NC_000913.3|_2_464-815 # 1ebf_A # 337 # 2799 '
'# 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs'
'_spacer=5-10bp;gc_cont=0.531'),
('QVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEEL'
'AQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMD'
'YYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDE'
'GMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNA'
'EGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKN'
'GENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLS'))
s4 = (('gi|556503834|ref|NC_000913.3|_2_816-820 # 337 # 2799 # 1 # ID='
'1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer='
'5-10bp;gc_cont=0.531', 'WKLGV'))
s5 = (('gi|556503834|ref|NC_000913.3|_2_462-820 # 337 # 2799 # 1 # ID'
'=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer='
'5-10bp;gc_cont=0.531'),
('TDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQE'
'ELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSS'
'MDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKL'
'DEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEF'
'NAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKV'
'KNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'))
s6 = (('gi|556503834|ref|NC_000913.3|_2_1-820 # 337 # 2799 # 1 # ID='
'1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer='
'5-10bp;gc_cont=0.531'), self.query)
obs = mask_sequence(self.file_a, self.file_query, None)
exp = {'match': [s1, s3], 'non_match': [s2, s4]}
self.assertEqual(obs, exp)
obs = mask_sequence(self.file_a, self.file_query, min_prob=100.0)
self.assertEqual(obs, {'match': [s1, s3], 'non_match': [s2, s4]})
obs = mask_sequence(self.file_a, self.file_query, max_evalue=4.1e-58)
self.assertEqual(obs, {'match': [s1], 'non_match': [s5]})
obs = mask_sequence(self.file_a, self.file_query, max_pvalue=1e-58)
self.assertEqual(obs, {'match': [s1], 'non_match': [s5]})
obs = mask_sequence(self.file_a,
self.file_query,
min_fragment_length=500)
self.assertEqual(obs, {'match': [], 'non_match': [s6]})
obs = mask_sequence(self.file_a,
self.file_query,
min_prob=99.0,
max_evalue=4.90e-41,
max_pvalue=0.00011,
min_fragment_length=200)
self.assertEqual(obs, {'match': [s1, s3], 'non_match': []})
obs = mask_sequence(self.file_a,
self.file_query,
min_prob=99.0,
max_evalue=4.90e-41,
max_pvalue=0.00011,
min_fragment_length=4)
self.assertEqual(obs, {'match': [s1, s3], 'non_match': [s4]})