Centromere statistics toolkit.
Project description
CenStats
Centromere statistics toolkit.
status
- Determine the status of centromeric contigs based on
RepeatMasker
annotations.
- Determine the status of centromeric contigs based on
length
- Estimate HOR array length from
stv
bed file andHumAS-HMMER
output.
- Estimate HOR array length from
Setup
pip install censtats
Usage
usage: censtats [-h] {status,length} ...
Centromere statistics toolkit.
positional arguments:
{status,length}
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
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