Comments (2)
Hi Keigo,
It is unfortunately not possible to use other input than a nucleotide fasta. But it's definitely something I should implement, but it will be some time before I have the time to implement.
Best,
Jakob
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I've made a pull request to allow to use GFF/Protein FASTA input instead of Prodigal, but it still needs the nucleotide FASTA for CRISPR arrays identification. For now it is only working with NCBI GFF, but making it work with prodigal should be easy
from crisprcastyper.
Related Issues (20)
- Complete genome and draft genome HOT 2
- A complement to CRISRPRCasFinder or its own thing? HOT 1
- Different results from CRISPR Cas typer web server and standalone version HOT 5
- Error when running cctyper: sed: cannot rename <output filename>/sed78a7GM: Permission denied HOT 2
- ![image](https://user-images.githubusercontent.com/121949837/212599561-d771b233-4bde-4850-8e5f-98a4164f78cb.png)
- Option to use Prodigal-gv
- Meaning of asterisk at the end of protein sequence HOT 1
- Creating empty files when there's no data HOT 1
- castyping.py having an issue with positional arguments. HOT 2
- CCTyper results HOT 4
- Orphan CRISPR definition HOT 2
- (Question) provide GFF file for pre computed gene calls? HOT 5
- XGBoost model incompatible HOT 8
- If minced detects a CRISPR with N's in the repeat sequence
- (Question) How can I plot svg post-hoc after a run? HOT 1
- ValueError: invalid literal for int() with base 10: 'lengt' HOT 2
- access to sequences that used to geenrate Cas profiles
- access to sequences that used to geenrate Cas profiles HOT 1
- error while loading shared libraries: libnsl.so.1
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