"""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['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)):
print record
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
yield curr
_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)):
print record
