modbampy
keenhl opened this issue · 2 comments
Thank for the for the prompt response. Here is the readme. I have did everything there and have tried multiple combinations of python and modbampy and I can't get anything to work.
Python package
A Python package is available on PyPI which contains basic functionality for parsing BAM files with modified-base information. It is envisaged that this will eventually be replaced by an implementation in pysam. As such the interface is supplements but does not integrate or replace pysam.
The package can be installed with:
pip install modbampy
The package contains simply to modes of use. Firstly an interface to iterate over reads in a BAM file and report modification sites:
from modbampy import ModBam
with ModBam(args.bam) as bam:
for read in bam.reads(args.chrom, args.start, args.end):
for pos_mod in read.mod_sites:
print(*pos_mod)
This project is now deprecated and will not be supported, please see the README for further details.
The readme doesn't provide any further details. That's what I'm trying to tell you