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#!/usr/bin/env python
# test_rdb.py
"""Unit test for RDB Parser
"""
from unittest import TestCase
from cogent3.core.info import Info
from cogent3.core.sequence import DnaSequence, RnaSequence, Sequence
from cogent3.parse.rdb import (
InfoMaker,
MinimalRdbParser,
RdbParser,
create_acceptable_sequence,
is_seq_label,
)
from cogent3.parse.record import RecordError
class RdbTests(TestCase):
"""Tests for top-level functions in Rdb.py"""
def test_is_seq_label(self):
"""is_seq_label should return True if a line starts with 'seq:'"""
seq = "seq:this is a sequence line"
not_seq = "this is not a sequence line"
still_not_seq = "this seq: is still not a sequence line"
self.assertEqual(is_seq_label(seq), True)
self.assertEqual(is_seq_label(not_seq), False)
self.assertEqual(is_seq_label(still_not_seq), False)
def test_create_acceptable_sequence(self):
"""create_acceptable_sequence: should handle 'o' and sec. struct"""
f = create_acceptable_sequence
# should keep any char accepted by RNA.alphabet.degen_gapped
s = "UCAG---NRYBDHKMNSRWVY?"
self.assertEqual(f(s), s)
# should replace 'o' by '?'
s = "UCAG-oo-ACGU"
self.assertEqual(f(s), "UCAG-??-ACGU")
# should strip out secondary info
s = "{UC^AG-[oo]-A(CG)U}"
self.assertEqual(f(s), "UCAG-??-ACGU")
# should leave other chars untouched
s = "XYZ1234"
self.assertEqual(f(s), "XYZ1234")
class InfoMakerTests(TestCase):
"""Tests for the Constructor InfoMaker. Should return an Info object"""
def test_empty(self):
"""InfoMaker: should return empty Info from empty header"""
empty_header = []
obs = InfoMaker(empty_header)
exp = Info()
self.assertEqual(obs, exp)
def test_full(self):
"""InfoMaker should return Info object with name, value pairs"""
test_header = [
"acc: X3402",
"abc:1",
"mty: ssu",
"seq: Mit. X3402",
"",
"nonsense",
":no_name",
]
obs = InfoMaker(test_header)
exp = Info()
exp.rRNA = "X3402"
exp.abc = "1"
exp.Species = "Mit. X3402"
exp.Gene = "ssu"
self.assertEqual(obs, exp)
class GenericRdbTest(TestCase):
"SetUp data for all Rdb parsers" ""
def setUp(self):
self.empty = []
self.labels = "mty:ssu\nseq:bac\n//\nttl:joe\nseq:mit\n//".split("\n")
self.nolabels = "ACGUAGCUAGCUAC\nGCUGCAUCG\nAUCG\n//".split("\n")
self.oneseq = "seq:H.Sapiens\nAGUCAUCUAGAUHCAUHC\n//".split("\n")
self.multiline = "seq:H.Sapiens\nAGUCAUUAG\nAUHCAUHC\n//".split("\n")
self.threeseq = "seq:bac\nAGU\n//\nseq:mit\nACU\n//\nseq:pla\nAAA\n//".split(
"\n"
)
self.twogood = "seq:bac\n//\nseq:mit\nACU\n//\nseq:pla\nAAA\n//".split("\n")
self.oneX = "seq:bac\nX\n//\nseq:mit\nACT\n//\nseq:pla\nAAA\n//".split("\n")
self.strange = "seq:bac\nACGUXxAaKkoo---*\n//".split("\n")
class MinimalRdbParserTests(GenericRdbTest):
"""Tests of MinimalRdbParser: returns (headerLines,sequence) tuples"""
def test_empty(self):
"""MinimalRdbParser should return empty list from file w/o seqs"""
self.assertEqual(list(MinimalRdbParser(self.empty)), [])
self.assertEqual(list(MinimalRdbParser(self.nolabels, strict=False)), [])
self.assertRaises(RecordError, list, MinimalRdbParser(self.nolabels))
def test_only_labels(self):
"""MinimalRdbParser should return empty list from file w/o seqs"""
# should fail if strict (the default)
self.assertRaises(RecordError, list, MinimalRdbParser(self.labels, strict=True))
# if not strict, should skip the records
self.assertEqual(list(MinimalRdbParser(self.labels, strict=False)), [])
def test_only_sequences(self):
"""MinimalRdbParser should return empty list form file w/o lables"""
# should fail if strict (the default)
self.assertRaises(
RecordError, list, MinimalRdbParser(self.nolabels, strict=True)
)
# if not strict, should skip the records
self.assertEqual(list(MinimalRdbParser(self.nolabels, strict=False)), [])
def test_single(self):
"""MinimalRdbParser should read single record as (header,seq) tuple"""
res = list(MinimalRdbParser(self.oneseq))
self.assertEqual(len(res), 1)
first = res[0]
self.assertEqual(first, (["seq:H.Sapiens"], "AGUCAUCUAGAUHCAUHC"))
res = list(MinimalRdbParser(self.multiline))
self.assertEqual(len(res), 1)
first = res[0]
self.assertEqual(first, (["seq:H.Sapiens"], "AGUCAUUAGAUHCAUHC"))
def test_multiple(self):
"""MinimalRdbParser should read multiple record correctly"""
res = list(MinimalRdbParser(self.threeseq))
self.assertEqual(len(res), 3)
a, b, c = res
self.assertEqual(a, (["seq:bac"], "AGU"))
self.assertEqual(b, (["seq:mit"], "ACU"))
self.assertEqual(c, (["seq:pla"], "AAA"))
def test_multiple_bad(self):
"""MinimalRdbParser should complain or skip bad records"""
self.assertRaises(RecordError, list, MinimalRdbParser(self.twogood))
f = list(MinimalRdbParser(self.twogood, strict=False))
self.assertEqual(len(f), 2)
a, b = f
self.assertEqual(a, (["seq:mit"], "ACU"))
self.assertEqual(b, (["seq:pla"], "AAA"))
def test_strange(self):
"""MRP: handle strange char. according to constr. and strip off '*'"""
f = list(MinimalRdbParser(self.strange))
obs = f[0]
exp = (["seq:bac"], "ACGUXxAaKkoo---")
self.assertEqual(obs, exp)
class RdbParserTests(GenericRdbTest):
"""Tests for the RdbParser. Should return Sequence objects"""
def test_empty(self):
"""RdbParser should return empty list from 'file' w/o labels"""
self.assertEqual(list(RdbParser(self.empty)), [])
self.assertEqual(list(RdbParser(self.nolabels, strict=False)), [])
self.assertRaises(RecordError, list, RdbParser(self.nolabels))
def test_only_labels(self):
"""RdbParser should return empty list from file w/o seqs"""
# should fail if strict (the default)
self.assertRaises(RecordError, list, RdbParser(self.labels, strict=True))
# if not strict, should skip the records
self.assertEqual(list(RdbParser(self.labels, strict=False)), [])
def test_only_sequences(self):
"""RdbParser should return empty list form file w/o lables"""
# should fail if strict (the default)
self.assertRaises(RecordError, list, RdbParser(self.nolabels, strict=True))
# if not strict, should skip the records
self.assertEqual(list(RdbParser(self.nolabels, strict=False)), [])
def test_single(self):
"""RdbParser should read single record as (header,seq) tuple"""
res = list(RdbParser(self.oneseq))
self.assertEqual(len(res), 1)
first = res[0]
self.assertEqual(first, Sequence("AGUCAUCUAGAUHCAUHC"))
self.assertEqual(
first.info,
Info({"Species": "H.Sapiens", "OriginalSeq": "AGUCAUCUAGAUHCAUHC"}),
)
res = list(RdbParser(self.multiline))
self.assertEqual(len(res), 1)
first = res[0]
self.assertEqual(first, Sequence("AGUCAUUAGAUHCAUHC"))
self.assertEqual(
first.info,
Info({"Species": "H.Sapiens", "OriginalSeq": "AGUCAUUAGAUHCAUHC"}),
)
def test_single_constructor(self):
"""RdbParser should use constructors if supplied"""
to_dna = lambda x, info: DnaSequence(str(x).replace("U", "T"), info=info)
f = list(RdbParser(self.oneseq, to_dna))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, "AGTCATCTAGATHCATHC")
self.assertEqual(
a.info, Info({"Species": "H.Sapiens", "OriginalSeq": "AGUCAUCUAGAUHCAUHC"})
)
def alternativeConstr(header_lines):
info = Info()
for line in header_lines:
all = line.strip().split(":", 1)
# strip out empty lines, lines without name, lines without
# colon
if not all[0] or len(all) != 2:
continue
name = all[0].upper()
value = all[1].strip().upper()
info[name] = value
return info
f = list(RdbParser(self.oneseq, to_dna, alternativeConstr))
self.assertEqual(len(f), 1)
a = f[0]
self.assertEqual(a, "AGTCATCTAGATHCATHC")
exp_info = Info(
{"OriginalSeq": "AGUCAUCUAGAUHCAUHC", "Refs": {}, "SEQ": "H.SAPIENS"}
)
self.assertEqual(
a.info,
Info({"OriginalSeq": "AGUCAUCUAGAUHCAUHC", "Refs": {}, "SEQ": "H.SAPIENS"}),
)
def test_multiple_constructor_bad(self):
"""RdbParser should complain or skip bad records w/ constructor"""
def dnastrict(x, **kwargs):
try:
return DnaSequence(x, **kwargs)
except Exception:
raise RecordError("Could not convert sequence")
self.assertRaises(RecordError, list, RdbParser(self.oneX, dnastrict))
f = list(RdbParser(self.oneX, dnastrict, strict=False))
self.assertEqual(len(f), 2)
a, b = f
self.assertEqual(a, "ACT")
self.assertEqual(a.info, Info({"Species": "mit", "OriginalSeq": "ACT"}))
self.assertEqual(b, "AAA")
self.assertEqual(b.info, Info({"Species": "pla", "OriginalSeq": "AAA"}))
def test_full(self):
"""RdbParser: full data, valid and invalid"""
# when only good record, should work independent of strict
r1 = RnaSequence(
"-??GG-UGAA--CGCU---ACGU-N???---",
info=Info(
{
"Species": "unidentified Thermus OPB AF027020",
"Refs": {"rRNA": ["AF027020"]},
"OriginalSeq": "-o[oGG-U{G}AA--C^GC]U---ACGU-Nooo---",
}
),
)
r2 = RnaSequence(
"---CGAUCG--UAUACG-N???-",
info=Info(
{
"Species": "Thermus silvanus X84211",
"Refs": {"rRNA": ["X84211"]},
"OriginalSeq": "---CGAU[C(G){--UA}U]ACG-Nooo-",
}
),
)
obs = list(RdbParser(RDB_LINES_ONLY_GOOD.split("\n"), strict=True))
self.assertEqual(len(obs), 2)
self.assertEqual(obs[0], r1)
self.assertEqual(str(obs[0]), str(r1))
self.assertEqual(obs[0].info, r1.info)
self.assertEqual(obs[1], r2)
self.assertEqual(str(obs[1]), str(r2))
self.assertEqual(obs[1].info, r2.info)
obs = list(RdbParser(RDB_LINES_ONLY_GOOD.split("\n"), strict=False))
self.assertEqual(len(obs), 2)
self.assertEqual(obs[0], r1)
self.assertEqual(str(obs[0]), str(r1))
self.assertEqual(obs[0].info, r1.info)
# when strict, should raise error on invalid record
f = RdbParser(RDB_LINES_GOOD_BAD.split("\n"), strict=True)
self.assertRaises(RecordError, list, f)
# when not strict, malicious record is skipped
obs = list(RdbParser(RDB_LINES_GOOD_BAD.split("\n"), strict=False))
self.assertEqual(len(obs), 2)
self.assertEqual(obs[0], r1)
self.assertEqual(str(obs[0]), str(r1))
self.assertEqual(obs[0].info, r1.info)
self.assertEqual(obs[1], r2)
self.assertEqual(str(obs[1]), str(r2))
self.assertEqual(obs[1].info, r2.info)
RDB_LINES_ONLY_GOOD = """acc:AF027020
seq: unidentified Thermus OPB AF027020
-o[oGG-U{G}AA--C^GC]U---ACGU-Nooo---
//
acc:X84211
seq: Thermus silvanus X84211
---CGAU[C(G){--UA}U]ACG-Nooo-
//
"""
RDB_LINES_GOOD_BAD = """acc:AF027020
seq: unidentified Thermus OPB AF027020
-o[oGG-U{G}AA--C^GC]U---ACGU-Nooo---
//
acc:ABC123
seq: E. coli
---ACGU-Nooo-RYXQ-
//
acc:X84211
seq: Thermus silvanus X84211
---CGAU[C(G){--UA}U]ACG-Nooo-
//
"""
|
