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
from crisprcastyper.
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)
- faa file of individual Cas proteins? HOT 7
- Multiple cctyper runs on the same contig giving different outputs? HOT 2
- Docker for cctyper HOT 1
- Problems running the program HOT 3
- add repeated sequence to repeats.fa HOT 1
- Expose minced options HOT 1
- Error in BLASTing for CRISPR near cas operons HOT 4
- CrisprCasTyper webserver HOT 1
- No database with conda install? HOT 2
- FileNotFoundError: blast.tab HOT 3
- 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
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from crisprcastyper.