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_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_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)
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_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))