No 'rU' option in Python 3.12 about teloclip

[Adamtaranto]

This issue was raised in issue #11 it is due to file read mode "rU" being removed in Python 3.11

I've fixed this on the main branch of this repo but haven't pushed updates to conda and pypi yet.

In the meantime, clone the repo and do a local pip install like this:
git clone https://github.com/Adamtaranto/teloclip.git && cd teloclip && pip install -e .

Or run in a conda env with an earlier version of Python.

[PengfeiInTuebingen]

Thanks for your reply, now it works with test data.
i am using my own data now, I got another issue:
[$]~> teloclip --ref V5.male.fasta.fai male.minimap2.sam
@pg ID:minimap2 PN:minimap2 VN:2.17-r941 CL:minimap2 -ax map-ont /ebio/scratch/fhaas/Ec_nanopore/Ec32/basecall_Ec32_modbase_all_super_V3/pass/Ec32_all.fasta V5.male.fasta
Reference sequence not found in FAI file: 58e481aa-cb3d-418f-9194-fc89512d369e
saying i didn't build index for my genome, actually i build the index(samtools faidx V5.male.fasta), do you have any idea about this?

[Adamtaranto]

Can you post the contents of your fai index file, and also the headers and first couple of alignments from your sam file.

[PengfeiInTuebingen]

Thanks a lot. I found an issue with my script, and now I have solved it. Thank you so much for the promotion!!!