Gert Hulselmans

icon company @aertslab icon location Bioinformatician in Laboratory of Computational Biology (part of KU Leuven Center for Human Genetics and the VIB Center for Brain and Disease Research.).

Results 446 comments of Gert Hulselmans

The rest of the queries?

Implementation for Pandas for 22 queries: https://gist.github.com/UranusSeven/55817bf0f304cc24f5eb63b2f1c3e2cd

Faster create_pseudobulks function.

It depends on how many ranges of the same value you have in a row. For `fragments_to_bw` it was at least 10 times faster, if I remember correctly. Do you...

Script "correct_barcode_in_fastq.sh" missing in newer image

It indeed does not contain `correct_barcode_in_fastq.sh` anymore as it was renamed to `correct_barcode_from_fastq.sh`. The newer version requires some more arguments than the old one. There is a newer version of...

Option to set a default delimiter

Maybe environment variables based on awk variable names would be a good idea: ``` XSV_FS = input field separator (input field delimiter) XSV_OFS = output field separator r (output field...

Option to set a default delimiter

@iliekturtles The bash function should be a a lot more complex than that. Some things that don't work: ``` $ xsvt -h Unknown flag: '-d' Usage: xsv [...] xsv [options]...

Numba Sort is Significantly Slower Than NumPy Sort

Codon now has a numpy implementation: https://www.exaloop.io/blog/codon-2025 They implemented multiple sorting algorithms for sorting numpy arrays: https://github.com/exaloop/codon/blob/develop/stdlib/numpy/sorting.codon ```python import numpy as np import numba import codon @numba.jit def sort_array_numba(x): return...