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dputhier / pygtftk

A python package and a set of shell commands to handle GTF files
GNU General Public License v3.0
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TypeError: a bytes-like object is required, not 'tuple' #152

Closed dputhier closed 3 years ago

dputhier commented 3 years ago

Hi @qferre , I think your last commits introduced an issue (maybe "Revised multiprocessing") . This command worked with commit dd6d23fa6d134822291d94b5271313258bc9c36d .

    gtftk ologram -z -f -w -q -c mm10 -p selected_tf/SRX2901288-Fos-Blood.bed  --more-bed `ls selected_tf/* | grep -vi fos`   --more-bed-multiple-overlap -k 16 -V 3  -j summed_bp_overlaps_pvalue -a summed_bp_overlaps_pvalue -g 0.05 -D -o SRX2901288-Fos

    concurrent.futures.process._RemoteTraceback:
    """
    Traceback (most recent call last):
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/concurrent/futures/process.py", line 239, in _process_worker
        r = call_item.fn(*call_item.args, **call_item.kwargs)
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/site-packages/pygtftk-1.2.8-py3.7-macosx-10.9-x86_64.egg/pygtftk/stats/intersect/overlap_stats_compute.py", line 413, in index_all_these
        oc.NPARRAY_which_combis_match_with(all_combis, combi, exact) for combi in combis_to_index
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/site-packages/pygtftk-1.2.8-py3.7-macosx-10.9-x86_64.egg/pygtftk/stats/intersect/overlap_stats_compute.py", line 413, in <listcomp>
        oc.NPARRAY_which_combis_match_with(all_combis, combi, exact) for combi in combis_to_index
      File "pygtftk/stats/intersect/overlap/overlap_regions.pyx", line 510, in pygtftk.stats.intersect.overlap.overlap_regions.__pyx_fuse_0NPARRAY_which_combis_match_with
      File "stringsource", line 658, in View.MemoryView.memoryview_cwrapper
      File "stringsource", line 349, in View.MemoryView.memoryview.__cinit__
    TypeError: a bytes-like object is required, not 'tuple'
    """

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

    Traceback (most recent call last):
      File "/Users/puthier/anaconda3/envs/python_dev_37/bin/gtftk", line 4, in <module>
        __import__('pkg_resources').run_script('pygtftk==1.2.8', 'gtftk')
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/site-packages/pkg_resources/__init__.py", line 665, in run_script
        self.require(requires)[0].run_script(script_name, ns)
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1463, in run_script
        exec(code, namespace, namespace)
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/site-packages/pygtftk-1.2.8-py3.7-macosx-10.9-x86_64.egg/EGG-INFO/scripts/gtftk", line 110, in <module>
        args = main()
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/site-packages/pygtftk-1.2.8-py3.7-macosx-10.9-x86_64.egg/EGG-INFO/scripts/gtftk", line 94, in main
        CmdManager.run(args)
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/site-packages/pygtftk-1.2.8-py3.7-macosx-10.9-x86_64.egg/pygtftk/cmd_manager.py", line 955, in run
        fun(**args)
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/site-packages/pygtftk-1.2.8-py3.7-macosx-10.9-x86_64.egg/pygtftk/plugins/ologram.py", line 950, in ologram
        multiple_overlap_custom_combis=multiple_overlap_custom_combis)
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/site-packages/pygtftk-1.2.8-py3.7-macosx-10.9-x86_64.egg/pygtftk/stats/intersect/overlap_stats_shuffling.py", line 491, in compute_overlap_stats
        multiple_overlap_custom_combis=multiple_overlap_custom_combis)
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/site-packages/pygtftk-1.2.8-py3.7-macosx-10.9-x86_64.egg/pygtftk/stats/intersect/overlap_stats_compute.py", line 978, in stats_multiple_overlap
        mappings.append(future.result())
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/concurrent/futures/_base.py", line 428, in result
        return self.__get_result()
      File "/Users/puthier/anaconda3/envs/python_dev_37/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
        raise self._exception
    TypeError: a bytes-like object is required, not 'tuple'
qferre commented 3 years ago

Fixed in the current develop branch. This was due to a commit I pushed by mistake.