def testTranslateAndCountHits(hits):
(total, counts) = countHits(hits)
myAssertEq(total,29)
myAssertEq(counts["Prochlorococcus"],10)
myAssertEq(counts['root'],7)
translateHits(hits,{'Bacteria <prokaryote>':'other','root':'other','Candidatus Pelagibacter':'Pelagibacter'})
myAssertEq(hits['000178_2410_1152'],['other'])
myAssertEq(hits['000093_2435_2228'],['Pelagibacter'])
def testTranslateAndCountHits(hits):
(total, counts) = countHits(hits)
myAssertEq(total, 29)
myAssertEq(counts["Prochlorococcus"], 10)
myAssertEq(counts['root'], 7)
translateHits(hits,
{'Bacteria <prokaryote>': 'other',
'root': 'other',
'Candidatus Pelagibacter': 'Pelagibacter'})
myAssertEq(hits['000178_2410_1152'], ['other'])
myAssertEq(hits['000093_2435_2228'], ['Pelagibacter'])
def testReadKoFile(koFile):
kPmap = readKOFile(koFile, "PATHWAY")
assert "K00397" not in kPmap
myAssertEq(kPmap["K00399"], ["ko00680 Methane metabolism", "ko01200 Carbon metabolism"])
kEmap = readKOFile(koFile, "EC")
myAssertEq(kEmap["K00397"], ["EC:1.8.99.-"])
myAssertEq(kEmap["K00399"], ["EC:2.8.4.1"])
def test_read_ncbi(ndir):
taxNames = True
taxonomy = readTaxonomy(ndir, taxNames)
taxIds = taxonomy.idMap
taxNames = taxonomy.nameMap
myAssertEq(len(taxIds), 783145)
myAssertEq(len(taxNames), 1101991)
# pick some random things to check
myAssertEq(taxIds[123456].name, 'Psammomoya choretroides')
myAssertIs(taxNames[simplifyString('Psammomoya choretroides')],
taxIds[123456])
myAssertIs(
taxNames[simplifyString('Psammomoya choretroides '
'(F.Muell.) Diels & Loes.')], taxIds[123456])
myAssertEq(taxIds[123499].parent.id, 50537)
return taxIds
def test_read_ncbi(ndir):
taxNames = True
taxonomy = readTaxonomy(ndir, taxNames)
taxIds = taxonomy.idMap
taxNames = taxonomy.nameMap
myAssertEq(len(taxIds), 783145)
myAssertEq(len(taxNames), 1101991)
# pick some random things to check
myAssertEq(taxIds[123456].name, 'Psammomoya choretroides')
myAssertIs(
taxNames[
simplifyString('Psammomoya choretroides')],
taxIds[123456])
myAssertIs(taxNames[simplifyString('Psammomoya choretroides '
'(F.Muell.) Diels & Loes.')],
taxIds[123456])
myAssertEq(taxIds[123499].parent.id, 50537)
return taxIds
def testParseHits(testFile):
# test line parsing methods
cells = [1, 2, 3, 4, "(4,5)", "6,7"]
(read, hitIter) = _getReadHitsSimple(cells, 0, 2, None)
hits = []
for h in hitIter:
hits.append(h)
myAssertEq(read, 1)
myAssertEq(len(hits), 1)
myAssertEq(hits[0], 3)
(read, hitIter) = _getReadHitsSep(cells, 1, 5, ',')
hits = []
for h in hitIter:
hits.append(h)
myAssertEq(read, 2)
myAssertEq(hits, ['6', '7'])
(read, hitIter) = _getReadHitsAll(list(cells), 3, -1, None)
hits = []
for h in hitIter:
hits.append(h)
myAssertEq(read, 4)
myAssertEq(len(hits), 5)
myAssertEq(hits, [1, 2, 3, "(4,5)", "6,7"])
# give it a test file
hitIter = parseHits(open(testFile), 0, -1, True, None)
hits = {}
for r, h in hitIter:
hits[r] = h
logging.debug(repr(hits))
myAssertEq(len(hits), 29)
myAssertEq(hits['000023_2435_2174'], ['Prochlorococcus'])
myAssertEq(hits['000178_2410_1152'], ['Bacteria <prokaryote>'])
myAssertEq(hits['000093_2435_2228'], ['Candidatus Pelagibacter'])
return hits
def testParseHits(testFile):
# test line parsing methods
cells = [1, 2, 3, 4, "(4,5)", "6,7"]
(read, hitIter) = _getReadHitsSimple(cells, 0, 2, None)
hits = []
for h in hitIter:
hits.append(h)
myAssertEq(read, 1)
myAssertEq(len(hits), 1)
myAssertEq(hits[0], 3)
(read, hitIter) = _getReadHitsSep(cells, 1, 5, ',')
hits = []
for h in hitIter:
hits.append(h)
myAssertEq(read, 2)
myAssertEq(hits, ['6', '7'])
(read, hitIter) = _getReadHitsAll(list(cells), 3, -1, None)
hits = []
for h in hitIter:
hits.append(h)
myAssertEq(read, 4)
myAssertEq(len(hits), 5)
myAssertEq(hits, [1, 2, 3, "(4,5)", "6,7"])
# give it a test file
hitIter = parseHits(open(testFile), 0, -1, True, None)
hits = {}
for r, h in hitIter:
hits[r] = h
logging.debug(repr(hits))
myAssertEq(len(hits), 29)
myAssertEq(hits['000023_2435_2174'], ['Prochlorococcus'])
myAssertEq(hits['000178_2410_1152'], ['Bacteria <prokaryote>'])
myAssertEq(hits['000093_2435_2228'], ['Candidatus Pelagibacter'])
return hits
def testReadKeggFile(keggFile):
kDmap = readKeggFile(keggFile, "DESCRIPTION")
myAssertEq(kDmap["K09630"], ["PRSS36; protease, serine, 36 [EC:3.4.21.-]"])
kPmap = readKeggFile(keggFile, "PATHWAY")
assert "K00397" in kPmap
myAssertEq(kPmap["K00399"], ["01200 Carbon metabolism", "00680 Methane metabolism", "01000 Enzymes"])
k2map = readKeggFile(keggFile, 2)
myAssertEq(k2map["K13810"][1].lower(), "Carbohydrate Metabolism".lower())
myAssertEq(k2map["K13810"][0].lower(), "Overview".lower())
myAssertEq(k2map["K00399"][1].lower(), "Energy Metabolism".lower())
myAssertEq(k2map["K00399"][0].lower(), "Overview".lower())
k3map = readKeggFile(keggFile, 3)
myAssertEq(
k3map["K13810"],
[
"01230 Biosynthesis of amino acids",
"00010 Glycolysis / Gluconeogenesis",
"00030 Pentose phosphate pathway",
"00500 Starch and sucrose metabolism",
"00520 Amino sugar and nucleotide sugar metabolism",
"01000 Enzymes",
"01000 Enzymes",
],
)
myAssertEq(k3map["K00399"], ["01200 Carbon metabolism", "00680 Methane metabolism", "01000 Enzymes"])
myAssertEq(k3map["K03404"], ["00860 Porphyrin and chlorophyll metabolism", "01000 Enzymes"])
myAssertEq(k3map["K01976"], ["01000 Enzymes"])
myAssertEq(
k3map["K07347"],
["02000 Transporters", "02044 Secretion system", "02035 Bacterial motility proteins", "05133 Pertussis"],
)
myAssertEq(k3map["K09630"], ["01000 Enzymes", "01002 Peptidases"])
k3mapQ = readKeggFile(keggFile, "3")
for k in k3map.iterkeys():
try:
myAssertEq(k3map[k], k3mapQ[k])
except AsserionError:
raise AssertionError("level 3 classes for %s do not match:\n%s\n%s" % (k, k3map[k], k3mapQ[k]))
def testParseGeneKOMap(koFile):
gkmap = parseGeneKOMap(koFile)
myAssertEq(gkmap["dpe:Dper_GL25993"], ["K00001"])
myAssertEq(gkmap["rpc:RPC_2974"], ["K00001"])
myAssertEq(gkmap["pic:PICST_59568"], ["K00100"])
myAssertEq(gkmap["bbp:BBPR_1508"], ["K02755", "K02756", "K02757"])
myAssertEq(gkmap["sfv:SFV_2242"], ["K02769", "K02770"])
myAssertEq(gkmap["fma:FMG_0161"], ["K02982"])
