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mtisza1 / DNA_methylase_finder

Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes
MIT License
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missing test files for nucleotides #3

Open c-ruprecht opened 2 weeks ago

c-ruprecht commented 2 weeks ago

Hey, I am trying to figure out some of the problems in your .sh script and might end up rewriting the pipeline using snakemake, would be very helpful to get the test .fna file that gives the output you show in the readme file. Thanks for any help, Constantin

mtisza1 commented 1 week ago

Constantin,

To address your immediate question, the reference sequences are available from the NCBI website with the listed accession number:

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016889925.1/

There are certainly a number of ways this tool could be improved from a scripting perspective and I'm happy to help in this endeavor if you are still planning to undertake it.

It may be worth checking first if these two new tools supercede DNA_methylase_finder:

https://github.com/cultivarium/MicrobeMod?tab=readme-ov-file#step-4-run-microbemod-annotate_rm

https://github.com/MicrobialDarkMatter/nanomotif?tab=readme-ov-file#mtase-linker

Best,

Mike