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abaizan / kodoja

Kodoja: identifying viruses from plant RNA sequencing data
MIT License
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Kodoja_build.py to update genomes #41

Closed mariferrarini closed 5 years ago

mariferrarini commented 5 years ago

Hi,

I was wondering if it's possible to add new genomes to the kodoja_db bypassing the ncbi download everytime. Let me explain: I already have my kodoja_db/ folder built and functional with viruses. However, if I run the kodoja_build.py again to add a new genome with "-e"/"-x" parameters, will the script try download the entire refseq genomes for the viruses?

Thank you very much, Sincerely, Mariana.

mariferrarini commented 5 years ago

Sorry for the multiple questions,

But also on the same subject, how to I add more than one custom genome to the kodoja_build.py and more than one file per genome? I tried to add three genomes, two of them contained .fna.gz and .faa.gz files, so I used -e/-x more than once in the command line and the script only kept the last input file given.

Thank you.

peterjc commented 5 years ago

There's an example using three genome files here:

https://github.com/abaizan/kodoja/blob/kodoja-v0.0.10/test/test_script.sh#L132

Note the use of -n or --no_download to avoid re-downloading.

Does that answer this?

mariferrarini commented 5 years ago

Yes, That covers everything, thank you very much.