pyBedGraph 0.1.1

An alternative to pyBigWig for bedgraph files

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:

# 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:

# 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:

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

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')