Metadata-Version: 2.1
Name: bgen
Version: 1.1.6
Summary: Package for loading data from bgen files
Home-page: https://github.com/jeremymcrae/bgen
Author: Jeremy McRae
Author-email: jmcrae@illumina.com
License: MIT
Description: ### Another bgen reader
        ![travis](https://travis-ci.org/jeremymcrae/bgen.svg?branch=master)
        
        This is a package for reading [bgen files](https://www.well.ox.ac.uk/~gav/).
        
        This package uses cython to wrap c++ code for parsing bgen files. It's not too
        slow, it can parse genotypes from 500,000 individuals at >100 variants per
        second within python.
        
        This has been primarily been designed around UKBiobank bgen files (i.e. bgen
        version 1.2 with zlib compressed genotype probabilities, but the other versions
        and compression schemes have also been tested using example bgen files).
        
        #### Install
        `pip install bgen`
        
        #### Usage
        ```python
        from bgen import BgenFile
        bfile = BgenFile(BGEN_PATH, sample_path=None)
        rsids = bfile.rsids()
        
        # select a variant by indexing
        var = bfile[1000]
        
        # pull out genotype probabilities
        probs = var.probabilities  # returns 2D numpy array
        dosage = var.minor_allele_dosage  # requires biallelic variant, returns numpy array
        
        # exclude variants from analyses by passing in indices
        to_drop = [1, 3, 500]
        bfile.drop_variants(to_drop)
        
        # pickle variants for easy message passing
        import pickle
        dumped = pickle.dumps(var)
        var = pickle.loads(dumped)
        
        # iterate through every variant in the file, without preloading every variant
        with BgenFile(BGEN_PATH, sample_path=None, delay_parsing=True) as bfile:
          for var in bfile:
              probs = var.probabilities
              dosage = var.minor_allele_dosage
              ploidy = var.ploidy
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
