Metadata-Version: 2.1
Name: camembert-bri
Version: 0.0.2
Summary: Python interface to BRI (Bam Read Index)
Home-page: https://github.com/usajusaj/camembertpy
Author: Matej Usaj
Author-email: m.usaj@utoronto.ca
License: UNKNOWN
Download-URL: https://github.com/usajusaj/camembertpy/archive/master.zip
Description: ![Python package](https://github.com/usajusaj/camembertpy/workflows/Python%20package/badge.svg)
        ![Python package build and publish](https://github.com/usajusaj/camembertpy/workflows/Python%20package%20build%20and%20publish/badge.svg)
        # camembertpy
        
        Cython wrapper for https://github.com/jts/bri with pysam integration.
        
        # Installation
        ## From pip repository
        ```bash
        pip install camembert-bri
        ```
        ## From source
        ### conda approach (recommended)
        ```bash
        conda env create -f environment.yml
        conda activate camembert
        python setup.py install
        ```
        ### pip approach
        ```bash
        # optional virtualenv:
        virtualenv camembert
        source camembert/bin/activate
        
        # Installation
        pip install -r requirements.txt
        python setup.py install
        ```
        
        # Examples
        ## API
        ### build read index
        ```python
        from camembert import Bri
        b = Bri(bam_file)
        b.create()
        ```
        
        ### retrieve reads
        ```python
        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
        ```bash
        camembert --help
        camembert <subcommand> --help
        ```
        
        ### build read index
        ```bash
        camembert index bam_file.bam
        ```
        
        ### retrieve reads
        ```bash
        camembert get bam_file.bam read_name
        ```
        
Keywords: bri samtools htslib read index
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
