def test_init_empty(self):
"""LOC empty init should succeed with expected defaults"""
l = LineOrientedConstructor()
self.assertEqual(l.Lines, [])
self.assertEqual(l.LabelSplitter(' ab cd '), ['ab', 'cd'])
self.assertEqual(l.FieldMap, {})
self.assertEqual(l.Constructor, MappedRecord)
self.assertEqual(l.Strict, False)
def test_empty_LOC(self):
"""LOC empty should fail if strict, fill fields if not strict"""
data = ["abc def", "3 n", "\t abc \txyz\n\n", "fgh "]
l = LineOrientedConstructor()
result = l()
self.assertEqual(result, {})
result = l([])
self.assertEqual(result, {})
result = l([' ', '\n\t '])
self.assertEqual(result, {})
result = l(data)
self.assertEqual(result, {'abc': 'xyz', '3': 'n', 'fgh': None})
def test_full_LOC(self):
"""LOC should behave as expected when initialized with rich data"""
data = [
"abc\t def", " 3 \t n", " abc \txyz\n\n", "x\t5", "fgh ",
"x\t3 "
]
class rec(MappedRecord):
Required = {'abc': []}
maps = {'abc': list_adder, 'x': int_setter, 'fgh': bool_setter}
label_splitter = DelimitedSplitter('\t')
constructor = rec
strict = True
loc_bad = LineOrientedConstructor(data, label_splitter, maps, \
constructor, strict)
self.assertRaises(FieldError, loc_bad)
strict = False
loc_good = LineOrientedConstructor(data, label_splitter, maps, \
constructor, strict)
result = loc_good()
assert isinstance(result, rec)
self.assertEqual(result, \
{'abc':['def','xyz'], '3':'n','fgh':False,'x':3})
def _sts_adder(obj, field, val):
"""Appends the current STS-type record to specified field"""
list_adder(obj, field, _read_sts(val))
def _seq_adder(obj, field, val):
"""Appends the current Sequence-type record to specified field"""
list_adder(obj, field, _read_seq(val))
def _protsim_adder(obj, field, val):
"""Appends the current ProtSim record to specified field"""
list_adder(obj, field, _read_protsim(val))
LinesToUniGene = LineOrientedConstructor()
LinesToUniGene.Constructor = UniGene
LinesToUniGene.FieldMap = {
'LOCUSLINK': int_setter,
'EXPRESS': _expressions_setter,
'PROTSIM': _protsim_adder,
'SCOUNT': int_setter,
'SEQUENCE': _seq_adder,
'STS': _sts_adder,
}
def UniGeneParser(lines):
"""Treats lines as a stream of unigene records"""
for record in GbFinder(lines):
curr = LinesToUniGene(record)
"""Sets specified field to a list of expressions"""
setattr(obj, field, semi_splitter(val))
def _sts_adder(obj, field, val):
"""Appends the current STS-type record to specified field"""
list_adder(obj, field, _read_sts(val))
def _seq_adder(obj, field, val):
"""Appends the current Sequence-type record to specified field"""
list_adder(obj, field, _read_seq(val))
def _protsim_adder(obj, field, val):
"""Appends the current ProtSim record to specified field"""
list_adder(obj, field, _read_protsim(val))
LinesToUniGene = LineOrientedConstructor()
LinesToUniGene.Constructor = UniGene
LinesToUniGene.FieldMap = {
'LOCUSLINK':int_setter,
'EXPRESS':_expressions_setter,
'PROTSIM':_protsim_adder,
'SCOUNT':int_setter,
'SEQUENCE':_seq_adder,
'STS':_sts_adder,
}
def UniGeneParser(lines):
"""Treats lines as a stream of unigene records"""
for record in GbFinder(lines):
curr = LinesToUniGene(record)
del curr['//'] #clean up delimiter
_ll_fieldmap['GO'] = _go_adder
_ll_fieldmap['EXTANNOT'] = _extannot_adder
_ll_fieldmap['MAP'] = _map_adder
_ll_fieldmap['CDD'] = _cdd_adder
_ll_fieldmap['ASSEMBLY'] = _assembly_adder
_ll_fieldmap['CONTIG'] = _contig_adder
for field in 'NG ACCNUM'.split():
_ll_fieldmap[field] = _accnum_adder
for field in 'NR NM NC NP XG XR XM XP PROT'.split():
_ll_fieldmap[field] = _accession_adder
for field in _ll_multi:
if field not in _ll_fieldmap:
_ll_fieldmap[field] = _generic_adder
LinesToLocusLink = LineOrientedConstructor()
LinesToLocusLink.Constructor = LocusLink
LinesToLocusLink.FieldMap = _ll_fieldmap
LinesToLocusLink.LabelSplitter = first_colon
def LocusLinkParser(lines):
"""Treats lines as a stream of unigene records"""
for record in LLFinder(lines):
curr = LinesToLocusLink(record)
yield curr
if __name__ == '__main__':
from sys import argv, stdout
filename = argv[1]
count = 0
for record in LocusLinkParser(open(filename)):
_ll_fieldmap['GO'] = _go_adder
_ll_fieldmap['EXTANNOT'] = _extannot_adder
_ll_fieldmap['MAP'] = _map_adder
_ll_fieldmap['CDD'] = _cdd_adder
_ll_fieldmap['ASSEMBLY'] = _assembly_adder
_ll_fieldmap['CONTIG'] = _contig_adder
for field in 'NG ACCNUM'.split():
_ll_fieldmap[field] = _accnum_adder
for field in 'NR NM NC NP XG XR XM XP PROT'.split():
_ll_fieldmap[field] = _accession_adder
for field in _ll_multi:
if field not in _ll_fieldmap:
_ll_fieldmap[field] = _generic_adder
LinesToLocusLink = LineOrientedConstructor()
LinesToLocusLink.Constructor = LocusLink
LinesToLocusLink.FieldMap = _ll_fieldmap
LinesToLocusLink.LabelSplitter = first_colon
def LocusLinkParser(lines):
"""Treats lines as a stream of unigene records"""
for record in LLFinder(lines):
curr = LinesToLocusLink(record)
yield curr
if __name__ == '__main__':
from sys import argv, stdout
filename = argv[1]
count = 0
for record in LocusLinkParser(open(filename)):