Question: Error in pysamstats
0
gravatar for PAn
2.3 years ago by
PAn20
United States
PAn20 wrote:

Hi,

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?

Thanks!

pysamstats jupyter python • 865 views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by PAn20

Did pysamstats imported properly? Can you test it in interactive mode of python?

ADD REPLYlink written 2.3 years ago by Vitis2.1k
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