Julian Libiseller-Egger
Julian Libiseller-Egger
Is it possible to use TempEst on a tree I don't have all the dates for or do I have to rebuild the tree with the subset of samples for...
Perhaps it's a known limitation, but I didn't find it in the README. When writing a `pd.DataFrame` to `.Rds`, the index is lost. Example: In Python ``` >>> import pandas...
I just tripped over a trailing single space (used as delimiter in these files) that is appended to every line in the *.mldist files after the final distance in the...
Hi there! IQ-TREE2 segfaulted on me for a large file. Top of logfile: ``` IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020 Developed by Bui Quang Minh,...
Is there a way of suppressing the `@POS` output for downstream variants and instead print the actual consequence, even though it is redundant?
Missing genotypes in variant files are ignored: https://github.com/mgalardini/pyseer/blob/2e27979568ee34f02d000ca3011002b9d399fb38/pyseer/input.py#L485-L486 However, in .Rtab files they are treated as missing data and the fit fails later on: https://github.com/mgalardini/pyseer/blob/2e27979568ee34f02d000ca3011002b9d399fb38/pyseer/input.py#L423-L424 Is this intended? For now...
When fitting an elastic net on .Rtab files that have columns with only zeros, pyseer gives the warning `No observations of [variant] in selected samples`, but the program completes. Therefore,...
It would be nice if we could pass a dict with custom annotations to the `qm.manhattanplot` function. For example, if I already know the IDs of my top hits and...
Many thanks for maintaining this great package! I have a large set of binary data (as `np.array` with type `bool`) for which I want to use a custom distance metric,...