biom-format/biom-format — pull request #61 by wasade (2012-12-02 23:01:45+00:00)
Title: bench scripts and standard bench tables

Bench table filenames are NxMxP_bench.biom, where N is the number of rows, M is the number of columns and P is the approximate nonzero percentage. This is approximate because the method for setting nonzero values has some overlap, leading to a slightly less nonzero count than the specified value of P.

The bench scripts simply load a table (argv[1], expectes gzip'd), and executes the described Table function. A wrapper call (such as Unix `time`) can provide information on runtime and memory consumption.

NOTE: bench_BASEPARSE.py just parses the table so the parse cost can be
ignored.

* added standard bench tables
* added code to make standard tables