def _get_ntgpadvals(self, flds, goid, nspc, add_ns):
"""Convert fields from string to preferred format for GPAD ver 2.1 and 2.0."""
is_set = False
qualifiers = self._get_qualifier(flds[2])
assert flds[3][:3] == 'GO:', 'UNRECOGNIZED GO({GO})'.format(GO=flds[3])
db_reference = self._rd_fld_vals("DB_Reference", flds[4], is_set, 1)
assert flds[5][:4] == 'ECO:', 'UNRECOGNIZED ECO({ECO})'.format(ECO=flds[3])
with_from = self._rd_fld_vals("With_From", flds[6], is_set)
taxons = self._get_taxon(flds[7])
assert flds[8].isdigit(), 'UNRECOGNIZED DATE({D})'.format(D=flds[8])
assert flds[9], '"Assigned By" VALUE WAS NOT FOUND'
props = self._get_properties(flds[11])
self._chk_qty_eq_1(flds, [0, 1, 3, 5, 8, 9])
# Additional Formatting
self._chk_qualifier(qualifiers)
# Create list of values
eco = flds[5]
goid = flds[3]
gpadvals = [
flds[0], # 0 DB
flds[1], # 1 DB_ID
qualifiers, # 3 Qualifier
goid, # 4 GO_ID
db_reference, # 5 DB_Reference
eco, # 6 ECO
ECO2GRP[eco],
with_from, # 7 With_From
taxons, # 12 Taxon
get_date_yyyymmdd(flds[8]), # 13 Date
flds[9], # 14 Assigned_By
get_extensions(flds[10]), # 12 Extension
props] # 12 Annotation_Properties
if add_ns:
gpadvals.append(nspc)
return gpadvals
def get_gafvals(self, flds, nspc):
"""Convert fields from string to preferred format for GAF ver 2.1 and 2.0."""
flds[3] = self._get_qualifier(flds[3]) # 3 Qualifier
flds[5] = self._get_set(flds[5]) # 5 DB_Reference
flds[7] = self._get_set(flds[7]) # 7 With_From
flds[8] = nspc # 8 GAF Aspect field converted to BP, MF, or CC
flds[9] = self._get_set(flds[9]) # 9 DB_Name
flds[10] = self._get_set(flds[10]) # 10 DB_Synonym
flds[12] = self._do_taxons(flds[12]) # 12 Taxon
flds[13] = get_date_yyyymmdd(flds[13]) # 13 Date 20190406
# Version 2.x has these additional fields not found in v1.0
if self.is_long:
flds[15] = get_extensions(flds[15]) # Extensions (or Annotation_Extension)
flds[16] = self._get_set(flds[16].rstrip())
else:
flds[14] = self._get_set(flds[14].rstrip())
return flds
def get_gafvals(self, flds, nspc):
"""Convert fields from string to preferred format for GAF ver 2.1 and 2.0."""
flds[3] = self._get_qualifier(flds[3]) # 3 Qualifier
flds[5] = self._get_set(flds[5]) # 5 DB_Reference
flds[7] = self._get_set(flds[7]) # 7 With_From
flds[8] = nspc # 8 GAF Aspect field converted to BP, MF, or CC
flds[9] = self._get_set(flds[9]) # 9 DB_Name
flds[10] = self._get_set(flds[10]) # 10 DB_Synonym
flds[12] = self._do_taxons(flds[12]) # 12 Taxon
flds[13] = get_date_yyyymmdd(flds[13]) # 13 Date 20190406
# Version 2.x has these additional fields not found in v1.0
if self.is_long:
flds[15] = get_extensions(flds[15]) # Extensions (or Annotation_Extension)
flds[16] = self._get_set(flds[16].rstrip())
else:
flds[14] = self._get_set(flds[14].rstrip())
return flds
def _get_ntgpadvals(self, flds, goid, nspc, add_ns):
"""Convert fields from string to preferred format for GPAD ver 2.1 and 2.0."""
is_set = False
qualifiers = self._get_qualifier(flds[2])
assert flds[3][:3] == 'GO:', 'UNRECOGNIZED GO({GO})'.format(GO=flds[3])
db_reference = self._rd_fld_vals("DB_Reference", flds[4], is_set, 1)
assert flds[5][:4] == 'ECO:', 'UNRECOGNIZED ECO({ECO})'.format(
ECO=flds[3])
with_from = self._rd_fld_vals("With_From", flds[6], is_set)
taxons = self._get_taxon(flds[7])
assert flds[8].isdigit(), 'UNRECOGNIZED DATE({D})'.format(D=flds[8])
assert flds[9], '"Assigned By" VALUE WAS NOT FOUND'
props = self._get_properties(flds[11])
self._chk_qty_eq_1(flds, [0, 1, 3, 5, 8, 9])
# Additional Formatting
if qualifiers:
self._chk_qualifier(qualifiers)
# Create list of values
eco = flds[5]
goid = flds[3]
gpadvals = [
flds[0], # 0 DB
flds[1], # 1 DB_ID
qualifiers, # 3 Qualifier
goid, # 4 GO_ID
db_reference, # 5 DB_Reference
eco, # 6 ECO
ECO2GRP[eco],
with_from, # 7 With_From
taxons, # 12 Taxon
get_date_yyyymmdd(flds[8]), # 13 Date
flds[9], # 14 Assigned_By
get_extensions(flds[10]), # 12 Extension
props
] # 12 Annotation_Properties
if add_ns:
gpadvals.append(nspc)
return gpadvals