make cut matrix AttributeError: 'Symbol' object has no attribute 'value'

[Zhiyi-Chen17]

Hi, rdalbanus，thanks for providing such a good tool.

(cutruntools2.1) chenzhiyi@luo-lab-tower:~/Software/CUT-RUNTools-2.0-master/install$ /home/chenzhiyi/.local/bin/make_cut_matrix -v -b '(25-150 1)' -d -o 0 -r 100 -p 1 -f 3 -F 4 -F 8 -q 0 /media/dell/data2/chenzhiyi/bulk-example-test/PRDM9/aligned/dedup.120bp/PRDM9.bam fimo.bed > fimo.cuts.freq.txt
Traceback (most recent call last):
File "/home/chenzhiyi/.local/bin/make_cut_matrix", line 277, in
make_cut_matrix(parse_arguments())
File "/home/chenzhiyi/.local/bin/make_cut_matrix", line 182, in parse_arguments
return parser.parse_args()
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 1734, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 1766, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 1972, in _parse_known_args
start_index = consume_optional(start_index)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 1912, in consume_optional
take_action(action, args, option_string)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 1824, in take_action
argument_values = self._get_values(action, argument_strings)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 2265, in _get_values
value = self._get_value(action, arg_string)
File "/home/chenzhiyi/miniconda3/envs/cutruntools2.1/lib/python3.6/argparse.py", line 2294, in _get_value
result = type_func(arg_string)
File "/home/chenzhiyi/.local/lib/python3.6/site-packages/atactk/command.py", line 126, in parse_bins
bin_string = bin_string.value()
AttributeError: 'Symbol' object has no attribute 'value'

[rdalbanus]

Hi @zyyyyy11144, thank you so much for using our tool! There might be something off with the invocation based on the errors thrown, but I cannot find anything explicitly wrong in your command.

Can you run the examples from the documentation in your data without any errors? E.g. make_cut_matrix -d -b '(36-149 150-324 325-400 1)' input.bam motif.bed.

If so, then one of your flags is causing the issue - I'd try adding them one by one to the example to see where it breaks.

If not, then it might be something with your input data. In that case:

1. Can you post the first 5 lines of the motif bed file?
2. What is the total number of lines in the motif bed file?
3. Is your bed file tab-separated? This may seem like a dumb question, but sometimes, the tabs are converted to spaces depending on how you process your files.