API reference

The Python API of crispr_analysis_utils, rendered from its docstrings.

Guide alignment

crispr_analysis_utils.guide_alignment finds every guide's genomic site; the guide explains how. The package re-exports the main names, such as guide_alignment.run. Module by module:

• pipeline: run, which chains every step, and its RunResult.
• library: reading the guide table, and writing the reads to align.
• scan: the genome pass, over the Rust core.
• sites: the Site record.
• orientation: the orientation verdicts.
• summary: the classes, and the output tables.
• iupac: IUPAC codes and PAM patterns.

Accession

• accession: accession ids for SpCas9 guides, encoded from the guide's own sequence.

Normalization

• counts_per_million

Utilities

• run_shell_cmd