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Commit ba340839 authored by Martin Larralde's avatar Martin Larralde
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Complete replacement of `t2pks.hmm` with `RREFam.hmm` in tests data

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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
AT - sp|Q9Y8A5|LOVB_ASPTE - 2.8e-31 100.1 0.3 2.8e-31 100.1 0.3 1.9 2 0 0 2 2 2 1 -
KS - sp|Q9Y8A5|LOVB_ASPTE - 1e-25 81.8 0.3 1e-25 81.8 0.3 1.8 2 0 0 2 2 2 1 -
CLF - sp|Q9Y8A5|LOVB_ASPTE - 1e-20 65.4 4.7 1.9e-20 64.5 4.7 1.3 1 0 0 1 1 1 1 -
CLF_8|9 - sp|Q9Y8A5|LOVB_ASPTE - 5.6e-14 43.0 3.1 1.1e-13 42.1 3.1 1.3 1 0 0 1 1 1 1 -
CLF_11|12 - sp|Q9Y8A5|LOVB_ASPTE - 7.4e-10 29.4 2.7 1.4e-09 28.4 2.7 1.4 1 0 0 1 1 1 1 -
CLF_7 - sp|Q9Y8A5|LOVB_ASPTE - 5.3e-09 26.6 3.0 1e-08 25.7 3.0 1.3 1 0 0 1 1 1 1 -
MET - sp|Q9Y8A5|LOVB_ASPTE - 1.9e-07 21.8 0.4 5.2e-07 20.4 0.0 1.9 2 0 0 2 2 2 1 -
KR - sp|Q9Y8A5|LOVB_ASPTE - 4.7e-06 17.9 0.1 0.00014 13.0 0.0 2.7 3 0 0 3 3 3 1 -
KR_C11 - sp|Q9Y8A5|LOVB_ASPTE - 0.00076 10.4 0.0 0.0023 8.8 0.0 1.8 1 1 0 1 1 1 1 -
KSIII - sp|Q8LDM2|PKSB_ARATH - 2.6e-12 37.8 0.0 2.4e-11 34.6 0.0 2.1 1 1 0 1 1 1 1 -
KSIII - sp|P9WPF1|PKS18_MYCTU - 1.6e-14 45.1 4.5 2.4e-09 28.1 1.8 2.3 2 0 0 2 2 2 2 -
KSIII - sp|O23674|PKSA_ARATH - 9.5e-08 22.8 0.0 1.4e-06 18.9 0.0 2.3 1 1 0 1 1 1 1 -
AT - sp|Q9ZGI2|PIKA4_STRVZ - 2e-48 156.5 12.7 6.2e-47 151.6 7.3 2.6 2 0 0 2 2 2 2 -
KS - sp|Q9ZGI2|PIKA4_STRVZ - 1.7e-37 120.6 5.1 5e-37 119.0 2.0 2.7 2 1 0 2 2 2 1 -
CLF - sp|Q9ZGI2|PIKA4_STRVZ - 3.6e-35 113.0 14.3 3.6e-35 113.0 14.3 2.0 2 0 0 2 2 2 1 -
CLF_8|9 - sp|Q9ZGI2|PIKA4_STRVZ - 1.1e-26 84.8 11.9 1.1e-26 84.8 11.9 2.1 2 0 0 2 2 2 1 -
CLF_11|12 - sp|Q9ZGI2|PIKA4_STRVZ - 1.7e-23 74.3 9.3 1.7e-23 74.3 9.3 2.1 2 0 0 2 2 2 1 -
CLF_7 - sp|Q9ZGI2|PIKA4_STRVZ - 3.9e-18 56.7 12.3 3.9e-18 56.7 12.3 2.2 3 0 0 3 3 3 1 -
ACP - sp|Q9ZGI2|PIKA4_STRVZ - 7.5e-07 20.7 0.0 2.2e-06 19.1 0.0 1.8 1 0 0 1 1 1 1 -
KSIII - sp|Q9ZGI2|PIKA4_STRVZ - 1 -0.3 11.5 0.38 1.0 5.9 2.8 2 1 0 2 2 2 0 -
KSIII - sp|Q4K418|PHLD_PSEF5 - 5.7e-15 46.5 3.9 2e-12 38.1 3.9 2.0 1 1 0 1 1 1 1 -
KS - sp|Q54FI3|STLB_DICDI - 3.3e-31 99.9 0.0 6.4e-30 95.6 0.0 2.4 1 1 0 1 1 1 1 -
AT - sp|Q54FI3|STLB_DICDI - 5.5e-24 76.1 0.0 9.1e-24 75.4 0.0 1.2 1 0 0 1 1 1 1 -
CLF - sp|Q54FI3|STLB_DICDI - 4.6e-21 66.5 0.0 8.2e-21 65.7 0.0 1.3 1 0 0 1 1 1 1 -
CLF_7 - sp|Q54FI3|STLB_DICDI - 6.9e-14 42.7 0.0 1.2e-13 42.0 0.0 1.2 1 0 0 1 1 1 1 -
CLF_8|9 - sp|Q54FI3|STLB_DICDI - 4.6e-13 40.0 0.0 7.6e-13 39.3 0.0 1.3 1 0 0 1 1 1 1 -
CLF_11|12 - sp|Q54FI3|STLB_DICDI - 7e-12 36.0 0.0 1.2e-11 35.3 0.0 1.3 1 0 0 1 1 1 1 -
ACP - sp|Q54FI3|STLB_DICDI - 1.3e-05 16.7 0.2 2.8e-05 15.6 0.2 1.5 1 0 0 1 1 1 1 -
AT - sp|Q9ZGI5|PIKA1_STRVZ - 2.1e-139 455.8 63.1 9.3e-56 180.6 19.1 3.8 3 0 0 3 3 3 3 -
KS - sp|Q9ZGI5|PIKA1_STRVZ - 3.9e-124 406.0 12.2 1e-43 141.0 0.2 4.9 3 1 0 3 3 3 3 -
CLF - sp|Q9ZGI5|PIKA1_STRVZ - 1.2e-101 331.9 61.6 2.3e-37 120.2 9.6 4.9 5 0 0 5 5 5 3 -
CLF_8|9 - sp|Q9ZGI5|PIKA1_STRVZ - 2.8e-77 251.5 42.2 3.6e-28 89.8 9.7 4.1 3 0 0 3 3 3 3 -
CLF_11|12 - sp|Q9ZGI5|PIKA1_STRVZ - 2.4e-61 198.9 45.9 1.3e-23 74.7 8.4 4.3 4 0 0 4 4 4 3 -
CLF_7 - sp|Q9ZGI5|PIKA1_STRVZ - 1.1e-53 173.7 54.1 5.6e-23 72.6 10.9 4.7 4 0 0 4 4 4 3 -
ACP - sp|Q9ZGI5|PIKA1_STRVZ - 1.6e-17 54.9 0.5 2e-08 25.7 0.1 3.8 3 0 0 3 3 3 3 -
KR_C11 - sp|Q9ZGI5|PIKA1_STRVZ - 2.1e-15 48.2 22.0 8e-10 30.0 2.4 4.2 4 0 0 4 4 4 2 -
KR - sp|Q9ZGI5|PIKA1_STRVZ - 3.9e-15 47.6 23.5 5.1e-11 34.1 8.0 5.5 7 0 0 7 7 2 2 -
KR_C19 - sp|Q9ZGI5|PIKA1_STRVZ - 1.5e-14 45.6 17.1 5.1e-11 34.0 0.7 3.6 4 0 0 4 4 4 2 -
KR_C9 - sp|Q9ZGI5|PIKA1_STRVZ - 1.8e-13 41.9 0.8 2.1e-07 22.0 0.1 2.6 2 0 0 2 2 2 2 -
KR_C17 - sp|Q9ZGI5|PIKA1_STRVZ - 2.6e-06 18.0 14.4 0.0001 12.7 1.1 2.9 2 0 0 2 2 2 2 -
DIMER - sp|Q9ZGI5|PIKA1_STRVZ - 0.001 9.8 18.3 0.00023 12.0 1.7 3.3 3 0 0 3 3 3 2 -
KR_C15 - sp|Q9ZGI5|PIKA1_STRVZ - 0.29 1.5 10.3 0.12 2.8 2.1 2.7 2 0 0 2 2 2 0 -
KSIII - sp|Q9ZGI5|PIKA1_STRVZ - 0.41 1.0 15.9 0.077 3.3 1.4 4.9 3 2 0 3 3 3 0 -
CLF - sp|A0A089QRB9|MSL3_MYCTU - 2.3e-43 139.9 8.3 7.4e-43 138.3 8.3 1.9 1 1 0 1 1 1 1 -
AT - sp|A0A089QRB9|MSL3_MYCTU - 4.3e-39 125.8 11.2 4.3e-39 125.8 11.2 2.3 2 0 0 2 2 2 1 -
KS - sp|A0A089QRB9|MSL3_MYCTU - 7.4e-37 118.5 0.6 7.4e-37 118.5 0.6 2.7 2 1 0 2 2 2 1 -
CLF_8|9 - sp|A0A089QRB9|MSL3_MYCTU - 1.8e-35 113.8 5.7 4.3e-35 112.5 5.7 1.6 1 0 0 1 1 1 1 -
CLF_7 - sp|A0A089QRB9|MSL3_MYCTU - 3.9e-31 99.5 8.6 8.7e-31 98.4 8.6 1.6 1 0 0 1 1 1 1 -
CLF_11|12 - sp|A0A089QRB9|MSL3_MYCTU - 4.3e-30 96.0 8.1 1.5e-29 94.3 8.1 1.9 1 1 0 1 1 1 1 -
KR - sp|A0A089QRB9|MSL3_MYCTU - 1.3e-08 26.2 7.0 1.3e-08 26.2 7.0 2.9 3 0 0 3 3 3 1 -
KR_C11 - sp|A0A089QRB9|MSL3_MYCTU - 3.9e-07 21.2 1.5 3.9e-07 21.2 1.5 3.0 3 0 0 3 3 3 1 -
KR_C9 - sp|A0A089QRB9|MSL3_MYCTU - 4.5e-07 20.9 0.3 4.5e-07 20.9 0.3 2.6 3 0 0 3 3 3 1 -
KR_C19 - sp|A0A089QRB9|MSL3_MYCTU - 7.7e-07 20.3 3.6 5.1e-06 17.6 0.2 2.6 2 0 0 2 2 2 1 -
ACP - sp|A0A089QRB9|MSL3_MYCTU - 3.4e-06 18.6 0.1 1.6e-05 16.4 0.0 2.2 2 0 0 2 2 2 1 -
CYC - sp|A0A089QRB9|MSL3_MYCTU - 0.0067 7.3 3.7 0.012 6.5 0.3 3.1 3 0 0 3 3 3 1 -
GT - sp|A0A089QRB9|MSL3_MYCTU - 4.7 -2.1 12.8 0.016 6.0 0.8 3.0 3 0 0 3 3 3 0 -
#
# Program: hmmscan
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SCAN
# Query file: pyhmmer/tests/data/seqs/PKSI.faa
# Target file: pyhmmer/tests/data/hmms/db/t2pks.hmm
# Option settings: hmmscan --tblout pyhmmer/tests/data/tables/t2pks.scan.tbl --domtblout pyhmmer/tests/data/tables/t2pks.scan.domtbl pyhmmer/tests/data/hmms/db/t2pks.hmm pyhmmer/tests/data/seqs/PKSI.faa
# Current dir: /home/althonos/Code/pyhmmer
# Date: Wed Nov 30 23:09:31 2022
# [ok]
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pyhmmer/tests/test_hmmer.py
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......@@ -703,6 +703,7 @@ class TestNhmmer(unittest.TestCase):
self.assertEqual(hits[0].best_domain.strand, "-")
self.assertEqual(hits[1].best_domain.strand, "-")
class TestHmmalign(unittest.TestCase):
def setUp(self):
self.tmpout = tempfile.NamedTemporaryFile(suffix=".hmm", delete=False).name
......
pyhmmer/tests/test_plan7/test_pipeline.py
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......@@ -240,19 +240,16 @@ class TestIteratePipeline(unittest.TestCase):
with SequenceFile(seq_path, digital=True, alphabet=cls.alphabet) as f:
cls.references = f.read_block()
query_path = resource_files(__package__).joinpath("data", "seqs", "LuxC.faa")
with SequenceFile(query_path, digital=True, alphabet=cls.alphabet) as f:
cls.query = next(seq for seq in f if b"P12748" in seq.name)
hmm_path = resource_files(__package__).joinpath("data", "hmms", "txt", "t2pks.hmm")
with HMMFile(hmm_path) as hmm_file:
cls.hmm = next(hmm for hmm in hmm_file if b"KR" in hmm.name)
def test_iterate_seq(self):
# check that `Pipeline.iterate_seq` produces consistent results
# compared to a 'gold standard' run of `jackhmmer`.
query_path = resource_files(__package__).joinpath("data", "seqs", "LuxC.faa")
with SequenceFile(query_path, digital=True, alphabet=self.alphabet) as f:
query = next(seq for seq in f if b"P12748" in seq.name)
pipeline = Pipeline(alphabet=self.alphabet, incE=0.001, incdomE=0.001)
search_iterator = pipeline.iterate_seq(self.query, self.references)
search_iterator = pipeline.iterate_seq(query, self.references)
for n in range(3):
self.assertEqual(search_iterator.iteration, n)
......@@ -280,8 +277,13 @@ class TestIteratePipeline(unittest.TestCase):
def test_iterate_hmm(self):
# check that `Pipeline.iterate_hmm` produces consistent results
# compared to a 'gold standard' run of `jackhmmer` (actually, manually iterated hmmsearches).
hmm_path = resource_files(__package__).joinpath("data", "hmms", "txt", "KR.hmm")
with HMMFile(hmm_path) as hmm_file:
hmm = hmm_file.read()
pipeline = Pipeline(alphabet=self.alphabet, incE=0.001, incdomE=0.001)
search_iterator = pipeline.iterate_hmm(self.hmm, self.references)
search_iterator = pipeline.iterate_hmm(hmm, self.references)
for n in range(6):
self.assertEqual(search_iterator.iteration, n)
......
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