pandas-plink
pandas-plink copied to clipboard
limix
PLINK reader for Python.
Hi developer, Thanks for developing this nice package. I was wondering if we have the plan to support plink2 format in the future. Thanks! Yanyu
Hi there, I was surprised to find a major error in your pandas-plink package! I used it to read /bed/bim/fam files into python. But I found that my minor alleles...
Dear Developers: I notice that after the last pandas-plink update, the memory needed to load the same amount of matrix significantly increase (during the process of lazy loading). I wonder...
Newer versions of pandas (2+) cause _write_bim and _write_fam to fail. This change ('line_terminator' -> 'lineterminator' in calls to pandas.DataFrame.to_csv) works for both new and old pandas versions.
This is a fix for https://github.com/limix/pandas-plink/issues/35.
Dask 2024.2 makes pandas-plink unusably slow (~4 hrs to read a 850 MB bed file). Due to [improved tokenization](https://docs.dask.org/en/stable/changelog.html#v2024-2-0), Dask now computes a sha1 hash of `buff` for each [call...
I'd like to read in plink data to `int8` arrays rather than `float32`. Looking at `_bed_read.py` it seems this could be done at the chunk level by modifying `_read_bed_chunk()`. Are...
I have Python 3.9.18 and Pandas 2.1.1. My pandas-Plink version is 2.2.9 **The command: write_plink1_bin(G_sample1, "sample1.bed") gives this error output: "TypeError: to_csv() got an unexpected keyword argument 'line_terminator'". The current...
Sorry if I'm doing something wrong, but when I use `plink2 ... --recode vcf` I get chromosomes called `21`, `22`, `X`, `Y` and even `MT`... However, using `read_plink(files)`, they are...
Passing a Python standard library `pathlib.Path` object to `read_plink` leads to: ``` TypeError: expected string or bytes-like object ```
