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 []