Mercurial > repos > melissacline > ucsc_cancer_utilities
comparison seg2matrix/CGData/BaseTable.py @ 52:3a036a34c362
better handle of input file
| author | jingchunzhu |
|---|---|
| date | Thu, 17 Sep 2015 15:00:45 -0700 |
| parents | b6f5d2d1b047 |
| children | b88b95642f59 |
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| 51:728eda331f07 | 52:3a036a34c362 |
|---|---|
| 61 if 'comment' in self['cgformat']: | 61 if 'comment' in self['cgformat']: |
| 62 comment = self['cgformat']['comment'] | 62 comment = self['cgformat']['comment'] |
| 63 linenum = 0 | 63 linenum = 0 |
| 64 for row in read: | 64 for row in read: |
| 65 linenum += 1 | 65 linenum += 1 |
| 66 if linenum ==1: #ignore header line | |
| 67 continue | |
| 66 r = self.__row_class__() | 68 r = self.__row_class__() |
| 67 if (comment is None or not row[0].startswith(comment)) and not row[0].startswith("#"): | 69 if (comment is None or not row[0].startswith(comment)) and not row[0].startswith("#"): |
| 68 for i, col in enumerate(cols): | 70 for i, col in enumerate(cols): |
| 71 skip =0 | |
| 69 isOptional = False | 72 isOptional = False |
| 70 if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'optional' in self['cgformat']['columnDef'][col]: | 73 if 'columnDef' in self['cgformat'] and col in self['cgformat']['columnDef'] and 'optional' in self['cgformat']['columnDef'][col]: |
| 71 isOptional = self['cgformat']['columnDef'][col]['optional'] | 74 isOptional = self['cgformat']['columnDef'][col]['optional'] |
| 72 if len(row) > i: | 75 if len(row) > i: |
| 73 try: | 76 try: |
| 74 setattr(r, col, colType[col](row[i])) | 77 setattr(r, col, colType[col](row[i])) |
| 75 except ValueError: | 78 except ValueError: |
| 76 raise ValueError( "col invalid type %s on line %d" % (row[i], linenum)) | 79 raise ValueError( "col invalid type %s on line %d" % (row[i], linenum)) |
| 77 else: | 80 else: |
| 78 if isOptional: | 81 if isOptional: |
| 79 setattr(r, col, None) | 82 setattr(r, col, None) |
| 80 else: | 83 else: |
| 81 print row | 84 print row |
| 85 skip =1 # ignore bad lines | |
| 86 break | |
| 82 raise InvalidFormat("missing colum " + col) | 87 raise InvalidFormat("missing colum " + col) |
| 83 | 88 if skip: |
| 89 continue | |
| 90 | |
| 84 if not self.groupKey: | 91 if not self.groupKey: |
| 85 if self.secondKey is not None: | 92 if self.secondKey is not None: |
| 86 key1 = getattr(r, self.firstKey ) | 93 key1 = getattr(r, self.firstKey ) |
| 87 key2 = getattr(r, self.secondKey ) | 94 key2 = getattr(r, self.secondKey ) |
| 88 if key1 not in storeMap: | 95 if key1 not in storeMap: |