christacaggiano / celfie Goto Github PK

hi Christa, our thesis student added a random seed flag for numpy in celfie to that the output is reproducible (https://github.com/rmvpaeme/celfie/blob/ad1ff869ad08cc382a84ff7addd0af59d74a1519/EM/em.py#L360). It might be interesting to add this to the main branch.

Dear Christa,
Thank you for developing celfie.
I am trying to apply the analysis to a very controlled dilution experiment we conducted, but I was puzzled to observe that celfie returned often negative fractions in the cell type estimation. Also, different runs lead to very different results (numerical instability?). Is this behaviour expected? I checked the input files and they seem to be fine.

I am deconvolving 20 samples simultaneously using 3 known pure components + 1 unknown, and other much simpler tools based on quadratic programming or regression on beta seem to easily capture the correct fractions up to few % of error.

Best

Hi Christa,

Thank you for developing CelFiE.

When I use the tim.sh to generate my own TIMs, I found the tim_summed.txt output file was not for regions but for CpG sites. After debugging, I found there is a code error in this line "awk -v window="$window_size" '{print $1 "\t" $2-$window "\t" $3+$window}' $output_file"sites" > $output_file""$window_size". It should be no $ before window inside awk.

Hope this is helpful.

Congratulations on the manuscript: https://www.biorxiv.org/content/10.1101/2020.01.15.907022v1"""

I think this is a really interesting concept.

It looks like you plan to put notebooks here at some point: https://github.com/christacaggiano/celfie/tree/master/jupyter_notebooks

Please update this issue when you do, as it would be great to see.

Best, Evan Biederstedt

Hello,

I'm trying to run CelFiE from the celfie_env conda enviroment

Command:
python /path/celfie/TIMs/tim.py input_path output 100 27 15 2

And I get the following output:

Traceback (most recent call last):
  File "/usr/local/hurcs/miniconda3/envs/python-3.7/lib/python3.7/site-packages/numpy/core/__init__.py", line 22, in <module>
    from . import multiarray
  File "/usr/local/hurcs/miniconda3/envs/python-3.7/lib/python3.7/site-packages/numpy/core/multiarray.py", line 12, in <module>
    from . import overrides
  File "/usr/local/hurcs/miniconda3/envs/python-3.7/lib/python3.7/site-packages/numpy/core/overrides.py", line 7, in <module>
    from numpy.core._multiarray_umath import (
ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/cs/icore/ekushele/celfie/TIMs/tim.py", line 2, in <module>
    import numpy as np
  File "/usr/local/hurcs/miniconda3/envs/python-3.7/lib/python3.7/site-packages/numpy/__init__.py", line 150, in <module>
    from . import core
  File "/usr/local/hurcs/miniconda3/envs/python-3.7/lib/python3.7/site-packages/numpy/core/__init__.py", line 48, in <module>
    raise ImportError(msg)
ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.9 from "/cs/icore/ekushele/miniconda3/envs/celfie_env/bin/python"
  * The NumPy version is: "1.21.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: No module named 'numpy.core._multiarray_umath'

My conda_env.yml file (I upgraded numpy to 1.21.3):

name: celfie
channels:
  - defaults
dependencies:
  - numpy=1.21.2
  - pandas
  - bottleneck
  - seaborn

Hi,

When I usu one sample, celfie runs well:

python celfie.py celfie_samples_combined_ref.txt dir 1

But when I try the same with two samples, it fails:

python celfie.py celfie_samples_combined_ref.txt dir 2

Here is the error message:

Traceback (most recent call last):
  File "celfie.py", line 373, in <module>
    alpha, gamma, ll = em(
  File "celfie.py", line 182, in em
    a, g = maximization(p0, p1, x, x_depths, y, y_depths)
  File "celfie.py", line 131, in maximization
    new_alpha[n, :] = np.dot(p1[:, :, n], x[n, :]) + np.matmul(
  File "<__array_function__ internals>", line 200, in dot
TypeError: can't multiply sequence by non-int of type 'float'

Input is in correct format. Do you have any idea what could go wrong here? Thanks

Hi Christa,

Thank you for developing CelFiE. I am trying to run CelFiE on 2 samples (adult normal lung tissues-WGBS). After getting the coverage file from Bismark, I ran your prepare_bismark.sh script and created the input to CelFiE with the reference TIMs you provided. I ran CelFiE using the following command for both samples:

python em.py SRR3269863_reference_file_tims.txt 00-deconvolution_with_celfie 1 1000 0 1 0.001 1
python em.py SRR3274240.2_reference_file_tims.txt 00-deconvolution_with_celfie 1 1000 0 1 0.001 100

However, the cell_proportions from CelFiE for both samples indicate >90% placenta which should not be the case.

I am attaching the input files here for each sample as well as the output from CelFiE. I assumed that the output array from the pickle file is ordered in the same way as your reference_file_key.txt.

SRR3269863_reference_file_tims.txt
SRR3274240.2_reference_file_tims.txt
CelFiE_deconvolution_results.xlsx

Any help will be appreciated.

Thanks, Fayaz