camembertpy

Cython wrapper for https://github.com/jts/bri with pysam integration.

Installation

From pip repository

pip install camembert-bri

From source

conda approach (recommended)

conda env create -f environment.yml
conda activate camembert
python setup.py install

pip approach

# optional virtualenv:
virtualenv camembert
source camembert/bin/activate

# Installation
pip install -r requirements.txt
python setup.py install

Examples

API

build read index

from camembert import Bri
b = Bri(bam_file)
b.create()

retrieve reads

from camembert import Bri
b = Bri(bam_file)
b.load()
for read in b.get(read_name):
    print(read.to_string())  # read is of type pysam.AligmentSegment

CLI

A command line interface is included and mimics the original bri CLI command. For usage, refer to

camembert --help
camembert <subcommand> --help

build read index

camembert index bam_file.bam

retrieve reads

camembert get bam_file.bam read_name