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Python interface to BRI (Bam Read Index)

Project description

Python package Python package build and publish


Cython wrapper for with pysam integration.


From pip repository

pip install camembert-bri

From source

conda approach (recommended)

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

pip approach

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

# Installation
pip install -r requirements.txt
python install



build read index

from camembert import Bri
b = Bri(bam_file)

retrieve reads

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


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

Project details

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Source Distribution

camembert-bri-0.0.2.tar.gz (58.3 kB view hashes)

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