Contig coverage from PB.cov

contig_cov.py

#!/usr/bin/env python
# encoding: utf-8
"""
Created by Brant Faircloth on May 9, 2024 at 14:00:38 CDT
Copyright (c) 2024 Brant C. Faircloth. All rights reserved.

Description: 

"""

#import pdb
import numpy
from collections import defaultdict

values = defaultdict(list)
with open("PB.base.cov") as infile:
    for line in infile:
        ls = line.strip()
        if line.startswith(">"):
            curr_contig = line.lstrip(">").split("\t")[0]
        else:
            cov =ls.split("\t")[2]
            values[curr_contig].append(int(cov))

for k,v in values.items():
    print(k,numpy.mean(v))