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)
_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)):
print record
_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)):
print record
