diced_py

Function init

Source 
pub fn init(_py: Python<'_>, m: Bound<'_, PyModule>) -> PyResult<()>
Expand description

PyO3 bindings to diced, a library for CRISPRs detection.

Diced is re-implementation of MinCED, a method developed by Connor T. Skennerton <https://github.com/ctSkennerton>_ to identify CRISPRs in isolate and metagenomic-assembled genomes. It was derived from the CRISPR recognition tool developed by Charles Bland et al..

Example: Load a genome from a FASTA file using Biopython::

    >>> import Bio.SeqIO
    >>> record = Bio.SeqIO.read("Aquifex_aeolicus_VF5.fna", "fasta")

Detect CRISPR regions with Diced using the default parameters::

    >>> import diced
    >>> for crispr in diced.scan(str(record.seq[:300000])):
    ...     print(
    ...         crispr.start,
    ...         crispr.end,
    ...         len(crispr.repeats),
    ...         crispr.repeats[0],
    ...     )
    156459 156767 5 GTTCCTAATGTACCGTGTGGAGTTGAAACC
    244560 244791 4 GTTTCAACTCCACACGGTACATTAGGAAC
    279263 279555 5 GTTTTAACTCCACACGGTACATTAGAAAC