uauy-lab/ibspy

Python library to identify Identical By State regions

ibspy's Issues

ValueError: 'IBSpy/kmerGWAS/kmer_gwas.pyx' doesn't match any files

I want to install the python package
but I get the following error message:

    Complete output (11 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/eb-nlpiPW/pip-req-build-rsg1qlle/setup.py", line 43, in <module>
        compiler_directives={'language_level': "3"}),
      File "$INSTALLPATH/lib/python3.6/site-packages/Cython/Build/Dependencies.py", line 972, in cythonize
        aliases=aliases)
      File "$INSTALLPATH/lib/python3.6/site-packages/Cython/Build/Dependencies.py", line 815, in create_extension_list
        for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern):
      File "$INSTALLPATH/lib/python3.6/site-packages/Cython/Build/Dependencies.py", line 114, in nonempty
        raise ValueError(error_msg)
    ValueError: 'IBSpy/kmerGWAS/kmer_gwas.pyx' doesn't match any files
    ----------------------------------------

I have tried it with pip3 and with the following command. python3 setup.py develop
but none of them did work.

unable to build singularity container, sklearn deprecated + test error

Hello,

I tried to create a singularity container from the definition file in #16 .
At first, I have to modify the definition file, as sklearn is not longer existing (or atleast is only an empty package).
So change sklearn to scikit-learn.
But now, the test step fails

Merging single values for matrix 0.23029708862304688 Gb
Converting to PyRanges
.....
======================================================================
ERROR: test_run_affinity_propagation (test_result_set.TestResultSet)
----------------------------------------------------------------------
multiprocess.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/multiprocess/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/usr/local/src/IBSpy-0.4.6/IBSpy/IBSpy_result_set.py", line 156, in
wrapped_function = lambda x: self._function_window_wrapper_tabix(x, function, chromosome, assembly = assembly)
File "/usr/local/src/IBSpy-0.4.6/IBSpy/IBSpy_result_set.py", line 116, in _function_window_wrapper_tabix
return function(m), chromosome, start, end
File "/usr/local/src/IBSpy-0.4.6/IBSpy/IBSpy_result_set.py", line 196, in run_single_run
raise ex
File "/usr/local/src/IBSpy-0.4.6/IBSpy/IBSpy_result_set.py", line 190, in run_single_run
runs = cluster_by_haplotype(gr, seed=seed, iterations=iterations, dampings=dampings, max_missing=max_missing, min_iterations=min_iterations)
File "/usr/local/src/IBSpy-0.4.6/IBSpy/window_affinity_propagation.py", line 168, in cluster_by_haplotype
desc_stats = descriptive_stats(gr)
File "/usr/local/src/IBSpy-0.4.6/IBSpy/window_affinity_propagation.py", line 121, in descriptive_stats
ret['skew'] = skew(melted['value'])
File "/usr/local/lib/python3.9/site-packages/scipy/stats/_axis_nan_policy.py", line 502, in axis_nan_policy_wrapper
res = hypotest_fun_out(*samples, **kwds)
File "/usr/local/lib/python3.9/site-packages/scipy/stats/_stats_py.py", line 1305, in skew
m2 = _moment(a, 2, axis, mean=mean)
File "/usr/local/lib/python3.9/site-packages/scipy/stats/_stats_py.py", line 1184, in moment
eps = np.finfo(a_zero_mean.dtype).resolution * 10
File "/usr/local/lib/python3.9/site-packages/numpy/core/getlimits.py", line 492, in new
raise ValueError("data type %r not inexact" % (dtype))
ValueError: data type <class 'numpy.object'> not inexact
"""

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

Traceback (most recent call last):
File "/usr/local/src/IBSpy-0.4.6/tests/test_result_set.py", line 165, in test_run_affinity_propagation
ret = ibspy_results.run_affinity_propagation()
File "/usr/local/src/IBSpy-0.4.6/IBSpy/IBSpy_result_set.py", line 214, in run_affinity_propagation
for best, chromosome, start, end in self.map_window_iterator_tabix(function= run_single_run, chromosome=chr):
File "/usr/local/src/IBSpy-0.4.6/IBSpy/IBSpy_result_set.py", line 160, in map_window_iterator_tabix
newlist = [x for x in res]
File "/usr/local/src/IBSpy-0.4.6/IBSpy/IBSpy_result_set.py", line 160, in
newlist = [x for x in res]
File "/usr/local/lib/python3.9/site-packages/multiprocess/pool.py", line 870, in next
raise value
ValueError: data type <class 'numpy.object_'> not inexact

----------------------------------------------------------------------

It would be nice from you to help me.

Regards
Jens

python3 setup.py test failed with 8 ERRORs

Hello,

I using setup.py test to test if the tool is installed properly. I have installed all the specified requirements. I get the following error message (for all of the tests):

ERROR: test_results (unittest.loader._FailedTest)

ImportError: Failed to import test module: test_results
Traceback (most recent call last):
File "/home/wicker/anaconda3/lib/python3.8/unittest/loader.py", line 436, in _find_test_path
module = self._get_module_from_name(name)
File "/home/wicker/anaconda3/lib/python3.8/unittest/loader.py", line 377, in _get_module_from_name
import(name)
File "/home/wicker/data1/matthias/IBSPY_test/IBSpy/tests/test_results.py", line 12, in
from IBSpy import IBSpyResults
File "/home/wicker/data1/matthias/IBSPY_test/IBSpy/IBSpy/init.py", line 8, in
from .IBSpy_result_set import IBSpyResultsSet
File "/home/wicker/data1/matthias/IBSPY_test/IBSpy/IBSpy/IBSpy_result_set.py", line 15, in
from .IBSpy_values_matrix import IBSpyValuesMatrix
File "/home/wicker/data1/matthias/IBSPY_test/IBSpy/IBSpy/IBSpy_values_matrix.py", line 17, in
class IBSpyValuesMatrix:
File "/home/wicker/data1/matthias/IBSPY_test/IBSpy/IBSpy/IBSpy_values_matrix.py", line 142, in IBSpyValuesMatrix
def merged_values(self) -> dict[str, pysam.TabixFile]:
TypeError: 'type' object is not subscriptable

Jellyfish load error

I can't get IBSpy to work with jellyfish input files: it dies immediately:
IBSpy -o "Rye_vs_CS_1B.tsv" -k 31 -d Rye.jf -r 1B.fa -w 50000 -f jellyfish
Traceback (most recent call last):
File "/Users/bzglab/opt/anaconda3/bin/IBSpy", line 11, in
load_entry_point('IBSpy', 'console_scripts', 'IBSpy')()
File "/Users/bzglab/Downloads/IBSpy-main/IBSpy/init.py", line 10, in main
window_count(parse_arguments())
File "/Users/bzglab/Downloads/IBSpy-main/IBSpy/IBSpy_window_count.py", line 42, in window_count
kmerdb = open_db(args)
File "/Users/bzglab/Downloads/IBSpy-main/IBSpy/IBSpy_window_count.py", line 32, in open_db
kmerdb = JellyfishSDB(args.kmer_size)
File "/Users/bzglab/Downloads/IBSpy-main/IBSpy/jellyfish_kmer_database.py", line 17, in init
raise ImportError("Jellyfish not loaded")
ImportError: Jellyfish not loaded

If I (wrongly) define -f kmerGWAS the program runs, but produces an output file with windows but zero matches so it seems the code is working to some extent. I'd prefer to use jellyfish as the kmerGWAS has a lot of dependencies!