CenStats 0.0.6

Centromere statistics toolkit.

CenStats

Centromere statistics toolkit.

• status
  • Determine the status of centromeric contigs based on RepeatMasker annotations.
• 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.

Setup

pip install censtats

Usage

usage: censtats [-h] {status,length,nonredundant} ...

Centromere statistics toolkit.

positional arguments:
  {status,length,nonredundant}

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