CRISPRCasTyper 1.9.0 – Python-native pipeline, bundled DB, and GFF/protein support.#66
CRISPRCasTyper 1.9.0 – Python-native pipeline, bundled DB, and GFF/protein support.#66pentamorfico wants to merge 10 commits intoRussel88:masterfrom
Conversation
|
Hi @Russel88, I wanted to follow up on PR #66 We are currently planning a new release that includes these changes, since the issues addressed in this PR are creating problems for downstream tool development on our side. Ideally, we would very much prefer to keep maintaining this tool in this repository, as the original upstream project, so that development remains centralized here and credit is clearly preserved. However, if the project is no longer being actively maintained, we will likely need to release a new version ourselves so that these fixes are publicly available and installable through PyPI and related channels. Before moving in that direction, I wanted to check whether the repository is still active and whether you would be open to reviewing or merging the PR. Happy to help with anything needed to move this forward. Best, |
Russel88
left a comment
Russel88
left a comment
There was a problem hiding this comment.
Did a quick review. Looks great. Small changes requested
| export CCTYPER_DB="/path/to/data/" | ||
| # or by using the --db argument each time you run CRISPRCasTyper: | ||
| cctyper input.fa output --db /path/to/data/ | ||
| mamba create -n cctyper bioconda::blast python>=3.10 |
There was a problem hiding this comment.
| mamba create -n cctyper bioconda::blast python>=3.10 | |
| mamba create -n cctyper bioconda::blast "python>=3.10" |
| cctyper input.fa output --db /path/to/data/ | ||
| mamba create -n cctyper bioconda::blast python>=3.10 | ||
| mamba activate cctyper | ||
| pip install git+https://github.com/pentamorfico/CRISPRCasTyper.git |
There was a problem hiding this comment.
To be updated on merge into main
| @@ -205,10 +188,8 @@ cctyper -h | |||
| * **hmmer.log** Error messages from HMMER (only produced if any errors were encountered) | |||
|
|
|||
There was a problem hiding this comment.
| * **crisprs.gff** GFF with CRISPR arrays | |
2 participants
This PR modernizes CRISPRCasTyper with a Python-native pipeline, bundled data/models, GFF/protein input, and updated install/docs. HMMER, prodigal, and minced dependencies are replaced by pyhmmer/pyhmmsearch, pyrodigal-gv, and diced; only BLAST+ remains external. The database and XGBoost models now ship inside the wheel/sdist, and CLI scripts/README are updated to recommend pip installs and document the new workflows.
Key changes
To do:
Version