An alternative to pyBigWig for bedgraph files
Project 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:
# 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 fastermod_approx_mean
- a slightly slower but more accurate approximate meanmax
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')
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distributions
No source distribution files available for this release.See tutorial on generating distribution archives.