pyd4 - Python Binding for D4 File Format
This python module allows python read D4 file.
Installation
Install through pip is recommended
pip install pyd4or you can also run the setup.py to install:
./setup.py installUsage by Example
from pyd4 import D4File
file = D4File("test.d4")
# Print the chrom list
print(file.chroms())
# Get the mean cov for region chr1:10000000-20000000
print(file.mean([("chr1", 10000000, 20000000)]))
# Get the depth distribution hisgoram for chr1:10000000-20000000.
# The max bucket is 1000 and the min bucket is 0
print(file.histogram([("chr1", 10000000, 20000000)], 0, 1000))
# Get a iterator over values
for i in file.value_iter("chr1", 0, 10000):
print(i)