pjvandehaar

#!/usr/bin/env python3

import asyncio
import sys

class StdOutProtocol(asyncio.SubprocessProtocol):
    def __init__(self, exit_future):
        self.exit_future = exit_future
        self.output = bytearray()
    def pipe_data_received(self, fd, data):

pjvandehaar

# resulting graph is at https://www.dropbox.com/s/vepdi2deoeejly0/dhs_nreads.png?dl=0

import pybedtools
import pysam
import itertools
import matplotlib.pyplot as plt

def avg(iterator):
    total, n = 0,0
    for it in iterator:

pjvandehaar

#!/usr/bin/env python3

def get_blks():
    import gzip
    # <http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz>
    with gzip.open('hg38ToHg19.over.chain.gz', 'rt') as f:
        for line in f:
            line = line.rstrip('\n').split()
            if line and line[0] == 'chain':
                blk = dict(chr1=line[2], std1=line[4], stt1=int(line[5]), len1=int(line[6]),