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LKremer / CAFE_fig

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)
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ZeroDivisionError: float division by zero #4

Open liufeibio opened 5 years ago

liufeibio commented 5 years ago

Hi, @LKremer I am trying to use CAFE_fig to visualize the results from CAFE, but I encountered some problems. Here is my running: python3 ./CAFE_fig/CAFE_fig.py cafe_result.cafe -c asc=vL, da -pb 0.05 -pf 0.05 --dump test/ -g .pdf --count_all_expansions And these are output:

Traceback (most recent call last): File "./CAFE_fig/CAFE_fig.py", line 517, in main(**vars(args)) File "./CAFE_fig/CAFE_fig.py", line 458, in main c = CAFE_fig(report_cafe, families, clades, pb, pf, dump, gfx_output_format, count_all_expansions) File "./CAFE_fig/CAFE_fig.py", line 86, in init self.parse_tree() File "./CAFE_fig/CAFE_fig.py", line 136, in parse_tree self.parse_lambdas(line) File "./CAFE_fig/CAFE_fig.py", line 209, in parse_lambdas self.lambda_colors[i] = torgb(math.log(lambda), min_l, max_l) File "./CAFE_fig/CAFE_fig.py", line 62, in to_rgb v = (v_abs - min_v) / (max_v - min_v) # scaled to a value between 0 and 1 ZeroDivisionError: float division by zero

Could you help with this? I appreciate your help. Thanks! Fei

LKremer commented 5 years ago

Hi @liufeibio , I added a quick fix to the issue, please let me know if it works for you. Best, Lukas

liufeibio commented 5 years ago

Thanks for your help with this. It solved this problem. But I encountered another problem: Writing test/summary.pdf Traceback (most recent call last): File "./CAFE_fig/CAFE_fig.py", line 520, in main(**vars(args)) File "./CAFE_fig/CAFE_fig.py", line 480, in main p_value = family.tree.search_nodes(id=node_id)[0].pvalue AttributeError: 'TreeNode' object has no attribute 'pvalue' Could you help with this? I appreciate your help. Thanks a lot!

Hua-CM commented 5 years ago

Thanks for your help with this. It solved this problem. But I encountered another problem: Writing test/summary.pdf Traceback (most recent call last): File "./CAFE_fig/CAFE_fig.py", line 520, in main(**vars(args)) File "./CAFE_fig/CAFE_fig.py", line 480, in main p_value = family.tree.search_nodes(id=node_id)[0].pvalue AttributeError: 'TreeNode' object has no attribute 'pvalue' Could you help with this? I appreciate your help. Thanks a lot!

Did you resolve it? I come across the same problem now.

liufeibio commented 4 years ago

Thanks for your help with this. It solved this problem. But I encountered another problem: Writing test/summary.pdf Traceback (most recent call last): File "./CAFE_fig/CAFE_fig.py", line 520, in main(**vars(args)) File "./CAFE_fig/CAFE_fig.py", line 480, in main p_value = family.tree.search_nodes(id=node_id)[0].pvalue AttributeError: 'TreeNode' object has no attribute 'pvalue' Could you help with this? I appreciate your help. Thanks a lot!

Did you resolve it? I come across the same problem now.

No, I haven't, it is still there.

LKremer commented 4 years ago

Hi @liufeibio and @Hua-CM, sorry for the late reply. I have two questions in order to narrow down the possible causes of the error. 1) Can you reproduce the example plot from the readme file (using example data and the command in the readme)? 2) if so, could you upload your input files here or send them to me via email (L.Kremer at dkfz.de)? Best, Lukas