CenStats

Centromere statistics toolkit.

• length
  • Estimate HOR array length from stv bed file and HumAS-HMMER output.
• nonredundant
  • Get a non-redundant list of centromeres based on HOR array length from two AS-HOR array length lists. Uses output from length command.
• entropy
  • Calculate Shannon index across a region from RepeatMasker repeats.
• self-ident
  • Calculate 1D or 2D self-sequence average nucleotide identity via a k-mer-based containment index. Built from ModDotPlot's source code.
• kmer-entropy
  • Calculate Shannon index from a fasta file across all windows and their kmer set.

Setup

pip install censtats

Usage

usage: censtats [-h] {length,nonredundant,entropy,self-ident,kmer-entropy} ...

Centromere statistics toolkit.

positional arguments:
  {length,nonredundant,entropy,self-ident,kmer-entropy}

options:
  -h, --help            show this help message and exit

Read the docs here.

Build

make venv && make build && make install
source venv/bin/activate && censtats -h

To run tests:

source venv/bin/activate && pip install pytest
pytest -s -vv