Metadata-Version: 2.1
Name: pyBedGraph
Version: 0.1
Summary: An alternative to pyBigWig for bedgraph files
Home-page: https://github.com/c0ver/pyBedGraph
Author: Henry Zhang
Author-email: henrybzhang.99@gmail.com
License: UNKNOWN
Description: # pyBedGraph
        
        pyBedGraph is an alternative to pyBigWig.
        
        # Features:
        
          - Finds mean, approximate mean, max, min, coverage, and standard deviation
        
        # Improvements:
          - Much faster
        
        # Usage:
        Create the object:
        ```python
        # Chromosome that is stored in object will be the first that appears in the bedgraph file if not given
        genome = Genome('bedgraph_file.bedgraph', 'chr1')
        
        # Specify a bin size (default is 64)
        genome = Genome('bedgraph_file.bedgraph', 'chr1', 128)
        ```
        
        Search from a file:
        ```python
        # Out file is optional, output goes to stdout if not given
        # Default statistic to find is mean
        genome.stats_from_file('intervals_to_search_for.txt', 'out.txt')
        ```
        
        Search from a list of intervals:
        ```python
        intervals = [
            [0, 100],
            [101, 200],
            [4, 100],
            [100000, 999999]
        ]
        print(genome.stats(intervals))
        # output is [value1, value2, value3, value4]
        ```
        
        Choose a specific statistic:
          - `mean`
          - `approx_mean` - an approximate mean that is around 4x faster
          - `mod_approx_mean` - a slightly slower but more accurate approximate mean
          - `max`
          - `min`
          - `coverage`
          - `std`
        ```python
        intervals = [
            [0, 100],
            [101, 200],
            [4, 100],
            [100000, 999999]
        ]
        genome.stats(intervals, 'approx_mean')
        genome.stats_from_file('intervals_to_search_for.txt', 'out.txt', 'std')
        ```
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
