def __init__(self, filename=None, hdr_only=False, prt=sys.stdout):
self.filename = filename
self.evobj = EvidenceCodes()
# Initialize associations and header information
self.hdr = None
self.associations = self.read_gaf(filename, hdr_only,
prt) if filename is not None else []
def test_evcode_picker():
"""Test that expected 3 letter codes are chosen when given: inc, exc for codes and groups"""
obj = EvidenceCodes()
# pylint: disable=superfluous-parens
act = obj.get_evcodes()
print('ALL POSITIVE CODES: {C}'.format(C=' '.join(sorted(act))))
assert 'ND' not in act and len(act) > 15, act
#
act = obj.get_evcodes({'Experimental'})
assert act == set(['EXP', 'IDA', 'IPI', 'IMP', 'IGI', 'IEP']), act
#
act = obj.get_evcodes({'Experimental'}, {'IEP'})
assert act == set(['EXP', 'IDA', 'IPI', 'IMP', 'IGI']), act
#
act = obj.get_evcodes({'Experimental', 'Similarity'}, {'IEP', 'IMR'})
exp = {
'EXP', 'IDA', 'IPI', 'IMP', 'IGI', 'ISS', 'ISO', 'ISA', 'ISM', 'IGC',
'IBA', 'IBD', 'IKR', 'IRD'
}
assert act == exp, act
#
act = obj.get_evcodes(None, {'IEA'})
exp = set(obj.code2nt)
exp.difference_update({'IEA', 'ND'})
assert act == exp, act.symmetric_difference(exp)
#
obj.prt_details()
obj.prt_summary_code()
print("**TEST PASSED")
def __init__(self, filename=None, hdr_only=False, prt=sys.stdout, **kws):
# kws: allow_missing_symbol
self.kws = {k:v for k, v in kws.items() if k in self.exp_kwdct}
self.filename = filename
self.evobj = EvidenceCodes()
# Initialize associations and header information
self.hdr = None
self.associations = self.read_gaf(filename, hdr_only, prt) if filename is not None else []
def __init__(self, filename=None, **kws):
# kws: allow_missing_symbol
self.filename = filename
self.evobj = EvidenceCodes()
# Read anotation file, store namedtuples:
# Gene2GoReader(filename=None, taxids=None):
# GafReader(filename=None, hdr_only=False, prt=sys.stdout, allow_missing_symbol=False):
# GpadReader(filename=None, hdr_only=False):
self.hdr = None
self.datobj = None
self.associations = self._init_associations(filename, **kws)
def _prt_evidence_codes(args):
if not {'--ev_help', '--ev_help_short'}.isdisjoint(args):
print('\nEVIDENCE CODE HELP: --ev_exc --ev_inc')
print('Use any of these group names, ')
print(
'like Experimental or Similarity or Experimental,Similarity,')
print(
'or evidence codes, like IEA or ISS,ISO,ISA in --ev_exc or --ev_inc:'
)
obj = EvidenceCodes()
if '--ev_help' in args:
print('')
obj.prt_details()
if '--ev_help_short' in args:
print('')
obj.prt_summary_code()
sys.exit(0)
def __init__(self, name, filename=None, **kws):
# kws: allow_missing_symbol
self.name = name # name is one of valid_formats
self.filename = filename
self.godag = kws.get('godag')
self.namespaces = kws.get('namespaces')
self.evobj = EvidenceCodes()
# Read anotation file, store namedtuples:
# Gene2GoReader(filename=None, taxids=None):
# GafReader(filename=None, hdr_only=False, prt=sys.stdout, allow_missing_symbol=False):
# GpadReader(filename=None, hdr_only=False):
self.hdr = None
self.datobj = None
# pylint: disable=no-member
self.associations = self._init_associations(filename, **kws)
# assert self.associations, 'NO ANNOTATIONS FOUND: {ANNO}'.format(ANNO=filename)
assert self.namespaces is None or isinstance(self.namespaces, set)
def test_ev():
"""Return GO associations from a GAF file. Download if necessary."""
evs = _get_evidencecodes('gene2go')
obj = EvidenceCodes()
missing = evs.difference(obj.code2nt)
assert not missing, 'MISSING({EV})'.format(EV=missing)
def __init__(self, filename=None, log=sys.stdout):
self.filename = filename
self.log = log
self.evobj = EvidenceCodes()
self.associations = self.read_gaf(
filename) if filename is not None else []
