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Add argument to handle circular topology
Fix bug with sequences containing only CRISPRs
Add xgboost repeat classifier training script Fix some minor bugs
Restructure typing of small operons
Bump up version to fix pypi error
Fix pandas version problem Optimize typing
Update plotting features Do not plot putative CRISPR-Cas anymore
Fix small bugs with sequences having no operons Add plotting features
Fix bug with orderings of gene names in plot
Added plotting feature, to automatically draw maps of CRISPR-Cas loci
* Fix bug with deleting of CRISPR file if there was only one CRISPR * Lower thresholds to become more sensitive
* Solve hybrid systems: Write in output if an operon seems to a combination of two or more subtypes * Put putative CRISPR-Cas in separate file * Split spacers in a file per CRISPR array * Do not print empty files * Ensure correct parts are re-run with `--redo_typing`
Include some defensive checks for edge cases
Add repeat typing script
* Add consensus subtyping based on both Cas operons and CRISPR repeats * Fix multiprocess problem for macOS
Add minced for CRISPR prediction, and add xgboost for prediction of subtype based on repeat sequence.
Extra checks of input
Complete makeover of scripts into a python module
Add arguments. Fix coverage calculation. The first fix create new problems with overlapping alignments, which is fixed in this version.
Update argument structure.
Fix problem with ORF-HMM alignments which were split across multiple lines in the HMMER output. Prior to this version only the best match was chosen, now coverage is summed across the domain alignments, solving problems with detection of fusion proteins
Input can now be a prodigal-formatted protein fasta, by adding the `--aa` argument