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A code complexity of 5 is very low. That said, it doesn't prevent us from merging, but does remind us to check for overly complex code early. If we would...

Hi @peterch405, I've tried to test this with the latest version (0.9.1) and cannot reproduce this. Did you spot the `.gz` extension in the filename? ``` genomepy install GRCh38.p13 -b...

Hey @Ahmed-Shibl, Glad to hear you like the tool! Genomepy can only install one genome at a time (since you may wish to specify your options for each). If you...

I've seen that error from time to time, but only on the server, and not consistently. Let me know if its reproducible! The `gtfToGenePred` bioconda [recipe](https://github.com/bioconda/bioconda-recipes/blob/6e78c287dc0748e5101a0fe4e52b27f8461cdeb4/recipes/ucsc-gtftogenepred/meta.yaml#L35) has an unpinned openssl...

genomepy does not (currently) support this. This snippet should do the trick: ```{python3} from pyfaidx import Fasta import re oldfa = '/path/to/genome.fa' newfa = '/path/to/sorted_genome.fa' def sorted_nicely( l ): """...

Assuming that with manage, you mean also applies this sorting to the support files (fa.sizes, gaps.bed & fa.fai). If so, you can run this after the previous code: ``` from...

Thank you for the offer, but I don't think this is a desired feature. Chromosomes are sorted by size, which all tools I know can use, and some tools might...

My bad, you're right about the default order. Inserting a sorting function into genomepy (as user) would however be equally complex to running the sorting afterward. And since we can't...

Hey ChaoXu, genomepy downloads metadata from the genome providers. I think your error occurred during this step. Here are some options to try: - Your specific error suggests to me...

Hey zhicheng, This error is happening while connecting to the UCSC database. Their host is "genome-mysql.soe.ucsc.edu" and port is 3306. Here are some workarounds in case this does not work:...