genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2022-10-25	Reshape column major genotype database storage correctly.	Arun Isaac
	* gn3/genodb.py (matrix): Reshape column major genotype database storage as ncols x nrows instead of as nrows x ncols.
2022-06-20	gn3: genodb: Retire get function.	Arun Isaac
	* gn3/genodb.py (get): Delete function. (matrix): Use db.txn.get instead of get.
2022-06-20	gn3: genodb: Match class and function names of GenotypeMatrix.	Arun Isaac
	* gn3/genodb.py (GenotypeMatrix): Match class and function names.
2022-06-20	gn3: genodb: Remove db, nrows and ncols fields from GenotypeMatrix.	Arun Isaac
	db is unused. nrows and ncols are available in the array and transpose numpy arrays. * gn3/genodb.py (GenotypeMatrix)[db, nrows, ncols]: Delete fields. * gn3/genodb.py (matrix): Do not initialize db, nrows and ncols fields.
2022-06-20	gn3: genodb: Mention reading entire matrix in module docstring.	Arun Isaac
	* gn3/genodb.py: Mention reading entire matrix in module docstring.
2022-06-17	gn3: genodb: Rename Matrix named tuple to GenotypeMatrix.	Arun Isaac
	* gn3/genodb.py (Matrix): Rename to GenotypeMatrix. (matrix): Update invocation of Matrix.
2022-06-17	gn3: genodb: Allow retrieval of the entire genotype matrix.	Arun Isaac
	* gn3/genodb.py: Document nparray in the module docstring. (nparray): New function.
2022-06-17	gn3: genodb: Read optimized storage for the current matrix.	Arun Isaac
	The genotype database now stores the current version of the matrix alone in a read-optimized form, while storing the older versions of the matrix in a more compressed form. We are only interested in the current version of the matrix. So, always use the read optimized storage. * gn3/genodb.py (Matrix)[row_pointers, column_pointers]: Delete fields. [array, transpose]: New fields. * gn3/genodb.py (matrix, row, column): Read from read-optimized storage. (vector_ref): Delete function.
2022-06-09	gn3: genodb: Remove blank line in module docstring.	Arun Isaac
	* gn3/genodb.py: Remove blank line in module docstring.
2022-06-09	gn3: genodb: Rewrite without classes.	Arun Isaac
	We rewrite genodb using only functions. This makes for much more readable code. * gn3/genodb.py: Rewrite without classes.
2022-06-08	gn3: genodb: Support reading columns.	Arun Isaac
	* gn3/genodb.py (Matrix.__init__): Retrieve column pointers from database. (row): Abstract out vector access code to ... (Matrix.__vector): ... here. (Matrix.column): New method.
2022-06-08	gn3: genodb: Read only the most recent genotype matrix.	Arun Isaac
	The genotype database format now supports versioning of matrices. So, we update genodb.py to return only the most recent genotype matrix. * gn3/genodb.py (GenotypeDatabase.matrix): Return only the most recent genotype matrix.
2022-06-08	gn3: genodb: Open genotype database in read-only mode.	Arun Isaac
	* gn3/genodb.py (GenotypeDatabase.__init__): Open genotype database in read-only mode.
2022-06-08	gn3: genodb: Do not create genotype database if it does not exist.	Arun Isaac
	* gn3/genodb.py (GenotypeDatabase.__init__): Do not create genotype database if it does not exist.
2022-06-08	gn3: genodb: Decide on little endianness.	Arun Isaac
	It has been decided that the genotype database will use little endianness wherever applicable. * gn3/genodb.py (Matrix.__init__): Remove TODO note to decide on endianness.
2022-06-08	gn3: genodb: Do not terminate database strings with null.	Arun Isaac
	* gn3/genodb.py (GenotypeDatabase.get_metadata, GenotypeDatabase.matrix): Do not terminate database strings with the null character.
2022-06-03	gn3: Add genodb.	Arun Isaac
	genodb is a tiny library to read our new genotype database file format. * gn3/genodb.py: New file.