when I run ''mictools null $X $ODIR/null_dist.txt''but encountered the following error:
AttributeError: 'DataFrame' object has no attribute 'as_matrix'
Any suggestions?

I didn't find an example of how to use this mictools python api. Is there a reference to the use of this mictools python api like http://minepy.sourceforge.net/docs/1.0.0/python.html?

Hello,

Thank you very much for all the work on the package minepy and all the tools in mictools

This isa conceptual issue for my own understanding I would say, not code use.

Why do we need to use multitest correction, while we are already testing the TICe against all the resampled TICe pvals?

Is it an addition from the https://academic.oup.com/gigascience/article/7/4/giy032/4958979 to be very conservative? is it also advised in the original procedure from http://jmlr.csail.mit.edu/papers/v17/15-308.html ?

Thank you very much for your help!

Best

Hey, Davidealbanese. Thanks for your awesome work. It seems all the usages in README.rst are written in the format of command lines. May I ask whether there is any python example in using this package? Looking forward to your reply. Thanks in advance! Have a nice day!

Dear Mr. Davide

I try the datasaurus dataset and it worked perfectly until the end. But when I try to use another dataset from https://data.mendeley.com/datasets/h3cgnj8hft/1, There are problems:

1. When enter this line command: mictools adjust $ODIR/pval.txt $ODIR the warning shown from numpy, but files pval_adj.txt and pi0_None.png were created.
   Applications/Anaconda/anaconda3/lib/python3.7/site-packages/numpy/lib/arraysetops.py:569: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison mask |= (ar1 == a)
2. On the next step when enter this line command: mictools strength $X $ODIR/pval_adj.txt $ODIR/strength.txt
   File "/Applications/Anaconda/anaconda3/lib/python3.7/site-packages/scripts/mictools_cmd.py", line 265, in strength thr, alpha, clumps) File "/Applications/Anaconda/anaconda3/lib/python3.7/site-packages/mictools/strength.py", line 119, in strength_cmd c=clumps) File "/Applications/Anaconda/anaconda3/lib/python3.7/site-packages/mictools/strength.py", line 84, in compute_strength mine.compute_score(x, y) File "minepy/mine.pyx", line 84, in minepy.mine.MINE.compute_score ValueError: Buffer has wrong number of dimensions (expected 1, got 2)
   file strenght.txt is empty
   

Thank you for your help.
Jimmy

FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead.
Xa = X.as_matrix()

Hello
When i run: mictools mergenull 00.txt 11.txt uu.txt ( note: 00.txt and 11.txt were generated by 'mictools null …', respectively) , i got the error message: AttributeError: module 'mictools' has no attribute 'mergenull'. Based on Win platform and Linux (py2.7 and 3.7). may I know what is the reason?
Looking forward to your reply，thanks.
Yours
Qiusheng WU

Hi there,

I've followed the the pip installation instructions, but encountered the following error:

Command "python setup.py egg_info" failed with error code 1 in /private/tmp/pip-install-nko9_ymy/matplotlib/

Any suggestions?

Cheers,

Siobhan

Hello, I'm following the docker install and usage instructions:

docker pull minepy/mictools
docker run --rm -t -i -v /Users/will/Documents/mictools:/mictools -w /mictools minepy/mictools /bin/bash

But when running any commands, I get this below message:

raceback (most recent call last):
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 655, in _build_master
ws.require(requires)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 963, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 854, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 1.12.1 (/usr/lib/python3/dist-packages), Requirement.parse('numpy>=1.14'), {'statsmodels'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/local/bin/mictools", line 6, in
from pkg_resources import load_entry_point
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3019, in
@_call_aside
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3003, in _call_aside
f(*args, **kwargs)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3032, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 657, in _build_master
return cls._build_from_requirements(requires)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 670, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 854, in resolve
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 1.12.1 (/usr/lib/python3/dist-packages), Requirement.parse('numpy>=1.14'), {'statsmodels'})

Is this a problem with the python version? I am running 2.7.16, but I thought the docker image included python3?

Thanks for your help!

Hey,
I'm unsure what the issue is here. I am able to run mictools null just fine, however when I need to run mictools pval I get the following error. Any idea how to fix this? Or is this something I need to take up with my systems administrator?

Error:

`Traceback (most recent call last):
File "/home1/nathanwi/.local/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3790, in get_loc
return self._engine.get_loc(casted_key)
File "index.pyx", line 152, in pandas._libs.index.IndexEngine.get_loc
File "index.pyx", line 181, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 7080, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 7088, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'None'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home1/nathanwi/.local/bin/mictools", line 8, in
sys.exit(cli())
File "/home1/nathanwi/.local/lib/python3.9/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home1/nathanwi/.local/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/scripts/mictools_cmd.py", line 177, in pval
mictools.pval.pval_cmd(xvars, null, output, labels, target, yvars, rowwise,
File "/home1/nathanwi/.local/lib/python3.9/site-packages/mictools/pval.py", line 145, in pval_cmd
obs_dist, obs, pval = compute_pval(X=X,
File "/home1/nathanwi/.local/lib/python3.9/site-packages/mictools/pval.py", line 96, in compute_pval
null_dist_cl = null_dist.loc[cl]
File "/home1/nathanwi/.local/lib/python3.9/site-packages/pandas/core/indexing.py", line 1153, in getitem
return self._getitem_axis(maybe_callable, axis=axis)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/pandas/core/indexing.py", line 1393, in _getitem_axis
return self._get_label(key, axis=axis)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/pandas/core/indexing.py", line 1343, in _get_label
return self.obj.xs(label, axis=axis)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/pandas/core/generic.py", line 4228, in xs
loc, new_index = index._get_loc_level(key, level=0)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/pandas/core/indexes/multi.py", line 3175, in _get_loc_level
indexer = self._get_level_indexer(key, level=level)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/pandas/core/indexes/multi.py", line 3276, in _get_level_indexer
idx = self._get_loc_single_level_index(level_index, key)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/pandas/core/indexes/multi.py", line 2865, in _get_loc_single_level_index
return level_index.get_loc(key)
File "/home1/nathanwi/.local/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3797, in get_loc
raise KeyError(key) from err
KeyError: 'None'
`

Hello, I am trying to use minepy/mictools in conda but can't seem to get it to run. The commands are below:

conda create --name mictools
conda activate mictools
conda install -c bioconda minepy

When then running any commands such as mictools or minepy on their own, it simply says command not found. Is there something I'm doing wrong?

Sorry if this is a silly question, I cannot find any documentation about using it in conda

Thanks