Python interface to BRI (Bam Read Index)
Project description
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
Project details
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