Implements reading of VCF files. More...
Inheritance diagram for cls.DefaultTable.CVcfTableReader:
Collaboration diagram for cls.DefaultTable.CVcfTableReader:
Public Member Functions | |
| def | __init__ (s, ffn) |
| Ctor. More... | |
| def | GetHeader (s) |
| Get the header of the table contained in the VCF file. More... | |
| def | GetHeaderSection (s) |
| Get header section (comments) of the VCF file. More... | |
| def | SetHeaderSection (s, headerSection) |
| Set the header section of the VCF file. More... | |
| def | ValidateVCF (s) |
| Perform some sanity checks on the VCF file. More... | |
 Public Member Functions inherited from cls.DefaultTable.CDefaultTableReader | |
| def | __iter__ (s) |
| Return the iterable object, needed for for/while loops. More... | |
| def | next (s) |
| def | IsEmpty (s, verbose=False) |
| Checks if a file is empty. More... | |
| def | GetHeader (s, verbose=False) |
| Get the first line of this file. More... | |
| def | GetLineNr (s) |
| Get current line number. More... | |
| def | GetReader (s) |
| Public Member Functions inherited from cls.DefaultTable.CDefaultTableBase | |
| def | IsValid (s) |
| Check if the object is ready for reading/writing. More... | |
| def | Close (s) |
| Close the file object associated with the file name. More... | |
Additional Inherited Members | |
| Static Public Attributes inherited from cls.DefaultTable.CDefaultTableBase | |
| COL_SEP = CSV_SEP; | |
| QUOTING = csv.QUOTE_NONE; | |
| string | ESCAPE_CHAR = "\\"; |
Detailed Description
Implements reading of VCF files.
Constructor & Destructor Documentation
◆ __init__()
| def cls.DefaultTable.CVcfTableReader.__init__ | ( | s, | |
| ffn | |||
| ) |
Ctor.
@param ffn Full path file name. If it is set to '-', the standard
input or output will be opened instead.
Reimplemented from cls.DefaultTable.CDefaultTableReader.
Member Function Documentation
◆ GetHeader()
| def cls.DefaultTable.CVcfTableReader.GetHeader | ( | s | ) |
Get the header of the table contained in the VCF file.
◆ GetHeaderSection()
| def cls.DefaultTable.CVcfTableReader.GetHeaderSection | ( | s | ) |
Get header section (comments) of the VCF file.
Comments are defined as the lines prior to the line that starts with
<tt>\#CHROM</tt>.
@return @c List of @c Strings. Each line is an entry in the list.
◆ SetHeaderSection()
| def cls.DefaultTable.CVcfTableReader.SetHeaderSection | ( | s, | |
| headerSection | |||
| ) |
Set the header section of the VCF file.
◆ ValidateVCF()
| def cls.DefaultTable.CVcfTableReader.ValidateVCF | ( | s | ) |
Perform some sanity checks on the VCF file.
The documentation for this class was generated from the following file:
- cls/DefaultTable.py
