I am trying to run pysamstats through a python script in jupyter, here is the code that I am trying to use :
from __future__ import division, print_function import numpy as np %matplotlib inline import matplotlib.pyplot as plt import sklearn import pysam import pysamstats fasta_filename = 'data/Pf3D7_v3.fa' # path to the reference genome FASTA file bam_filename = 'data/Dd2.bam' # path to the BAM file containing aligned sequence reads fasta = pysam.Fastafile(fasta_filename) bam = pysam.Samfile(bam_filename) chrom = 'Pf3D7_05_v3' # chromosome 5 window_size = 300 # use 300bp non-overlapping windows coverage = pysamstats.load_coverage_ext_binned(bam, fasta, chrom=chrom, pad=True, window_size=window_size) coverage
But the pysamstats.load_coverage_ext_binned is giving me this error -
AttributeError Traceback (most recent call last) <ipython-input-18-5bdb4812a1d5> in <module>() 3 chrom = 'Pf3D7_05_v3' # chromosome 5 4 window_size = 300 # use 300bp non-overlapping windows ----> 5 coverage = pysamstats.load_coverage_ext_binned 6 coverage AttributeError: 'module' object has no attribute 'load_coverage_ext_binned'
I tried to correct this lot and wen through the modules list as well, but I cannot resolve it.
Can anyone please suggest?