Ilya Flyamer
Ilya Flyamer
Thank you. Is there a way to perform this, but still use genomepy to manage the new sorted genome?
OK, thank you! Would this feature be something you might be interested in? I might try to make a PR to add it then. The ordering of chromosomes is pretty...
Are chromosomes sorted by size? That's not what I experienced, for me they were sorted alphabetically, as I indicated in the first post. I'm not suggesting necessarily natural sorting, but...
Doesn't need to be a function, just the actual list of chromosome names in the right order would work.
No worries, I understand if this functionality might be not the most important. My main use-case is that I want to use genomepy in a pipeline to manage the genome...
Apologies for not replying to the original question. I am wondering about the reason you need this? You can easily extract just one chromosome from a whole-genome cooler file for...
What do you mean by a "multi-weighted" file? Which weights do you have there?
Then try using the `clr_weight_name` argument with one of these values https://cooltools.readthedocs.io/en/latest/cooltools.html#cooltools.api.eigdecomp.eigs_cis
Oh right, I forgot - cooltools doesn't support divisive weights at the moment, sorry! You could manually invert it and save a new weight...
Can you show example of the data? Or share the cooler? That sounds like there is something very weird going on with your data...