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nanoporetech / tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

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Problem importing Tombo in python

MarioRinBarr opened this issue · comments

commented

Hello,

I am trying to use the DENA package, which uses Tombo. However, when importing Tombo ("from tombo import tombo_helper, tombo_stats, resquiggle"; not even when using any of its functions) it totally fails. Does anyone know what could be going on here?

line 21, in
from tombo import tombo_helper, tombo_stats, resquiggle
File "/home/mario/anaconda3/lib/python3.11/site-packages/tombo/tombo_stats.py", line 84, in
HALF_NORM_EXPECTED_VAL = stats.halfnorm.expect()
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mario/anaconda3/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py", line 2914, in expect
dub = integrate.quad(fun, d, ub, **kwds)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mario/anaconda3/lib/python3.11/site-packages/scipy/integrate/_quadpack_py.py", line 465, in quad
retval = _quad(func, a, b, args, full_output, epsabs, epsrel, limit,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mario/anaconda3/lib/python3.11/site-packages/scipy/integrate/_quadpack_py.py", line 579, in _quad
return _quadpack._qagie(func,bound,infbounds,args,full_output,epsabs,epsrel,limit)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mario/anaconda3/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py", line 2891, in fun
return x * self.pdf(x, *args, **lockwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mario/anaconda3/lib/python3.11/site-packages/scipy/stats/_distn_infrastructure.py", line 1992, in pdf
place(output, cond, self._pdf(*goodargs) / scale)
^^^^^^^^^^^^^^^^^^^^
File "/home/mario/anaconda3/lib/python3.11/site-packages/scipy/stats/_continuous_distns.py", line 4253, in _pdf
return np.sqrt(2.0/np.pi)np.exp(-xx/2.0)
^^^^^^^^^^^^^^^^
FloatingPointError: underflow encountered in exp

commented

This package is deprecated. Remora is recommended for signal level analyses now. You may have some luck moving to an older numpy package if you require this method, but this package is not actively developed right now.