Mailman 3 September 2020 - fastlmm-user

Release of PySnpTools 0.4.19
by Carl KADIE July 3, 2021

July 3, 2021

Greetings, We're released a new version of PySnpTools (0.4.19). Here are the new features: * Bug fixed in the "Bgen" reader<https://fastlmm.github.io/PySnpTools/#module-pysnptools.distreader>. It has now has been tested on files as large 487,400 individuals x 4,840,000 SNPs (the size of the UK Biobank imputed genotype data). It should work with even larger files. * New option when reading from "Bed"<https://fastlmm.github.io/PySnpTools/#snpreader-bed> files directly into "… [View More]

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New releases of FaST-LMM and PySnpTools
by Carl KADIE July 3, 2021

July 3, 2021

I’m happy to announce a new releases of FaST-LMM<https://pypi.org/project/fastlmm/> and PySnpTools<https://pypi.org/project/pysnptools/>. (This release been my “work” since I retired last summer.) The new releases updates both packages to work with the newest version of Pandas, Numpy, and Scikit-learn. The new FaST-LMM release includes single_snp_scale, which allows FaST-LMM to use a cluster and scale to 1 million individuals. See Kadie and Heckerman, bioRxiv 2018<https://www.… [View More]

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New FaST-LMM Version: 4.0.11
by Carl KADIE Sept. 23, 2020

Sept. 23, 2020

Greetings, I'm happy to announce a new version of FaST-LMM. Install from https://pypi.org/project/fastlmm/. What's New: * Support for Python 3.8 The new version allows FaST-LMM to work with Anaconda's recent Python 3.8 release. FaST-LMM now runs on Python 3.7 and 3.8, on Linux, Windows, and Mac. * The single_snp function now supports per chromosome precomputed similarity matrices and covariates. https://fastlmm.github.io/FaST-LMM/#single-snp * Via the new PySnpTools, up … [View More]

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PySnpTools 4.0.22
by Carl KADIE Sept. 17, 2020

Sept. 17, 2020

Greetings, I'm happy to announce the release of PySnpTools 4.0.22. Upgrade with: pip install --upgrade pysnptools This version offers new multithreaded reading for both the PLINK BED format and the BGEN format. On my 6 processor machine, on UK Biobank-like data, it now reads 111 giant SNPs/sec & 162M probabilities/second (was 30 SNPs and 46M probs). * Carl

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'bed-reader': A New Standalone PLINK 1.9 .bed Reader & Writer
by Carl KADIE Sept. 8, 2020

Sept. 8, 2020

Greetings, I'm happy to announce a new standalone reader and writer for the PLINK .bed format. See https://pypi.org/project/bed-reader/. Example: >>> from bed_reader import open_bed, sample_file >>> >>> file_name = sample_file("small.bed") >>> bed = open_bed(file_name) >>> val = bed.read() >>> print(val) [[ 1. 0. nan 0.] [ 2. 0. nan 2.] [ 0. 1. 2. 0.]] >>> del bed Compared to the PySnpTools's Bed reader, the … [View More]

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