Greetings,

I’m happy to announce PySnpTools version 0.5.3. The new features were all at user request. The features are available to any program that uses PySnpTools, including FaST-LMM.

The new features are:

• The Bed reader can now handle non-numeric chromosome names, for example, “X” and “Y”. Likewise, the Bed writer can handle non-numeric chromosomes names.
• The Bed reader can now use *.fam and *.bim files with non-standard names.
• The SnpMemMap writer can now get data from any SnpReader, not just the in-memory SnpData. This, for example, allows even low-memory machines to create terabyte-sized memory-mapped files from *.bed files.
• The Dat reader can skip lines at the top of the file.

For details, see the PySnpTools documentation.

• (Bonus:  Bed-Reader which used to have an undocumented function for low-memory computers to create SNP-similarity matrices from memory-mapped files, now has an undocumented function to create kinship matrices from memory-mapped files. Let me know if you want details.)

You can get the new features with:

pip uninstall pysnptools

pip install pysnptools

Thanks for the great suggestions!

Yours,

Carl and the FaST-LMM team