Beispiel #1
0
 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
Beispiel #2
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    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
Beispiel #3
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    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
Beispiel #4
0
 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