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philippdre / omniCLIP

omniCLIP is a CLIP-Seq peak caller
GNU General Public License v3.0
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TypeError: 'numpy.float64' object cannot be interpreted as an integer #25

Open peaceben opened 3 years ago

peaceben commented 3 years ago

Hi philippdre,

executing run_omniclip using the parsed background and CLIP files gives me an TypeError (see below).

But I think i'm probably loosing my way already during the setup process. After following the installation guide i was not able to run omniclip by calling: python3 omniCLIP.py ( ModuleNotFoundError: No module named 'omniCLIP.data_parsing'; 'omniCLIP' is not a package). But i was able to call omniCLIP from my path (in the conda environment). Any thoughts?

Best, Ben

(omniEnv) linux@linux-Precision-T5600:~/omniCLIP$ omniCLIP run_omniCLIP --db-file ChrC_CLIP --bg-dat CP29A_background --clip-dat CP29A_CLIP --out-dir /home/linux/Desktop/CLIPbam Loading gene annotation Initialising the parameters

Iteration: 0 Computing most likely path Fitting emission parameters Fitting emission parameters Adds pseudo gene to prevent singular matrix during GLM fitting Estimating expression parameters Start estimation of expression parameters Constructing GLM matrix Estimating expression parameters: GLM matrix constrution Fitting GLM Estimating expression parameters: before fitting Finished expression parameter estimation Computing sufficient statistic for fitting md Getting suffcient statistic Fitting md distribution Estimating state 0 Estimating state 1 Estimating state 2 Estimating state 3 Fitting transition parameters Fitting transition parameters Learning transition model Iterating over genes .Traceback (most recent call last): File "/home/linux/anaconda3/envs/omniEnv/bin/omniCLIP", line 33, in sys.exit(load_entry_point('omniCLIP==0.2.0', 'console_scripts', 'omniCLIP')()) File "/home/linux/anaconda3/envs/omniEnv/lib/python3.7/site-packages/omniCLIP-0.2.0-py3.7-linux-x86_64.egg/omniCLIP/omniCLIP.py", line 560, in main run_omniCLIP(args) File "/home/linux/anaconda3/envs/omniEnv/lib/python3.7/site-packages/omniCLIP-0.2.0-py3.7-linux-x86_64.egg/omniCLIP/omniCLIP.py", line 98, in run_omniCLIP verbosity=EmissionParameters['verbosity']) File "/home/linux/anaconda3/envs/omniEnv/lib/python3.7/site-packages/omniCLIP-0.2.0-py3.7-linux-x86_64.egg/omniCLIP/omniCLIP.py", line 210, in PerformIteration verbosity=verbosity) File "/home/linux/anaconda3/envs/omniEnv/lib/python3.7/site-packages/omniCLIP-0.2.0-py3.7-linux-x86_64.egg/omniCLIP/omni_stat/trans.py", line 97, in FitTransistionParameters verbosity=verbosity) File "/home/linux/anaconda3/envs/omniEnv/lib/python3.7/site-packages/omniCLIP-0.2.0-py3.7-linux-x86_64.egg/omniCLIP/omni_stat/trans.py", line 186, in FitTransistionParametersSimple for n in range(n_iter): TypeError: 'numpy.float64' object cannot be interpreted as an integer

retrogenomics commented 3 years ago

same problem for me using miniconda3 on macos. In (omniEnv):

$ python3 ~/Lab/bioinfo/tools/omniCLIP/omniCLIP/omniCLIP.py generateDB --gff-file hg38_refGene.gtf --db-file hg38_refGene.db
Traceback (most recent call last):
  File "/Users/gcristof/Lab/bioinfo/tools/omniCLIP/omniCLIP/omniCLIP.py", line 30, in <module>
    from omniCLIP.data_parsing import tools
  File "/Users/gcristof/Lab/bioinfo/tools/omniCLIP/omniCLIP/omniCLIP.py", line 30, in <module>
    from omniCLIP.data_parsing import tools
ModuleNotFoundError: No module named 'omniCLIP.data_parsing'; 'omniCLIP' is not a package
adomingues commented 3 years ago

I also ran into this issue. Did you find a solution @retrogenomics ?

retrogenomics commented 3 years ago

@adomingues no unfortunately...