search

morris-lab / CellOracle

This is the alpha version of the CellOracle package
Other
316 stars 56 forks source link

Problems with ma.get_tss_info function #179

Closed niklasbinder closed 10 months ago

niklasbinder commented 10 months ago

tss_annotated = ma.get_tss_info(peak_str_list=peaks, ref_genome="hg38")

tss_annotated.tail()

NotImplementedError Traceback (most recent call last) Cell In[16], line 2 1 ##!! Please make sure to specify the correct reference genome here ----> 2 tss_annotated = ma.get_tss_info(peak_str_list=peaks, ref_genome="hg38") 4 # Check results 5 tss_annotated.tail()

File ~/miniconda3/envs/celloracle/lib/python3.8/site-packages/celloracle/motif_analysis/tss_annotation.py:75, in get_tss_info(peak_str_list, ref_genome, verbose, custom_tss_file_path) 72 queue = list_peakstr_to_df(peak_str_list) 73 queue = BedTool.from_dataframe(queue) ---> 75 annotated = annotate_tss(tss_ref_bed=ref, queue_bed=queue, verbose=verbose) 77 return annotated

File ~/miniconda3/envs/celloracle/lib/python3.8/site-packages/celloracle/motif_analysis/tss_annotation.py:105, in annotate_tss(tss_ref_bed, queue_bed, verbose) 102 raise ValueError("queue bed file error") 104 # intersect --> 105 intersected = tss_ref_bed.intersect(queue_bed, wb=True) 106 intersected = intersected.to_dataframe() 108 # change name

File ~/miniconda3/envs/celloracle/lib/python3.8/site-packages/pybedtools/bedtool.py:909, in BedTool._log_to_history..decorated(self, *args, kwargs) 905 def decorated(self, *args, *kwargs): 906 907 # this calls the actual method in the first place; result is 908 # whatever you get back --> 909 result = method(self, args, kwargs) 911 # add appropriate tags 912 parent_tag = self._tag

File ~/miniconda3/envs/celloracle/lib/python3.8/site-packages/pybedtools/bedtool.py:244, in _wraps..decorator..not_implemented_func(*args, *kwargs) 243 def not_implemented_func(args, **kwargs): --> 244 raise NotImplementedError(help_str)

NotImplementedError: "intersectBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method.

Fucicii commented 4 months ago

Hello, may I ask how you solved this problem, reinstall BEDtools?

niklasbinder commented 4 months ago

yes, it took a few attempts of reinstalling and restarting.

Fucicii commented 4 months ago

Thank you for your reply. I was a little unsure before, but it was solved after reinstalling.