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PySnpTools - A New Open Source Library for Reading & Manipulating Matrix Data


Anyone who uses fast numeric NumPy arrays but would like a simpler-than-Pandas ability to slice-and-dice, read-and-write will find PySnpTools useful. I'll describe PySnpTools and also tell how it fits into our Machine Learning research group's long-term move from C++/VB to C# to Python. I'll also show how we use PySnpTools in FaST-LMM to do state-of-the-art Genome Wide Association Studies.

The tutorial will cover: PstReader: Full NumPy-meets-Pandas-like slicing and subsetting of matrix data before (and after) reading from disk. (For genomics, it includes support for the PLINK Bed and phenotype formats. It also includes low-memory, high-speed methods for common operations such as standardization and kernel-creation.)

Utilities: One line intersecting and re-ordering of data for machine learning and statistics. Faster-than-NumPy extraction of a subarray from a NumPy array.

IntRangeSet: Manipulate from zero to billions of integers as sets with very little memory.

Python Trade Offs We Observe: Our industrial research group focuses on Machine Learning. Over 15 years, we have moved from C++/VB to C# to Python. I'll talk about why we choose Python and what tradeoffs we see.

Application: PySnpTools spun out of FaST-LMM. FaST-LMM is an Open Source, Python-based state-of-the-art system for doing Genome Wide Association Studies (GWAS). It is described in publications in Nature Methods, Nature Genetics, and Bioinfomatics.


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