Python API library and command line tools for GDC MAF files.
Read how to contribute here.
To clone the repository: git clone [email protected]:NCI-GDC/maf-lib.git.
To install locally: python setup.py install.
The MAF API can be found in maflib/.
Documentation can be generated using your favorite python documentation
tool, such as pydoc.
The library includes but is not limited to the following modules:
| Module | Description |
|---|---|
maflib.reader |
a module for reading MAF file |
maflib.writer |
a module for writing MAF files |
maflib.header |
a module for data stored in a MAF header, including but not limited to the version, annotation specification, sort order, and column names |
maflib.record |
a module to store a single line of the MAF file, or more specifically, the annotation values for a single mutation |
maflib.column |
a module to store a possibly typed column value for a MAF record |
maflib.column_types |
a module containing custom types for columns in a MAF file |
maflib.column_values |
a module containing custom enumeration values for columns in a MAF file |
maflib.schemes |
a module containing the schemes for a MAF file, determining the number of columns, their names, and their expected values |
maflib.sort_order |
a module containing the available sort orders to order records in a MAF file. |
maflib.sorter |
a module containing an implementation of a disk-backed sorting system. |
maflib.validation |
a module for the underlying validation of values stored in MAF files. |
maflib.overlap_iter |
a module containing an implementation of an iterator over MAF records that overlap across multiple MAF files. |
maflib.locatable |
a module containing interfaces for "locatable" MAF records, namely those that have a genomic span |
The GDC has specific "schemes" that determine the number of columns, their names, and their expected values.
Pre-defined schemes can be found in the src/maflib/resources directory.
The following schemes are natively supported:
| Scheme Name | Type | Inherits From |
|---|---|---|
| gdc.1.0.0 | Basic | None |
| gdc.1.0.0-protected | Protected | gdc.1.0.0 |
| gdc.1.0.0-public | Public | gdc.1.0.0-protected |
| gdc.1.0.1-protected | Protected | gdc.1.0.0 |
| gdc.1.0.1-public | Public | gdc.1.0.1-protected |