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vaquerizaslab / tadtool

TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
MIT License
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Can't use window_sizes in tadtool plot #29

Open Ziwei-Liu opened 6 months ago

Ziwei-Liu commented 6 months ago

I'm running a tadtool command as : tadtool plot lvan_20000.matrix lvan_20000_abs.bed LG14:9000000-10000000 -w window.txt -m 2000000

But it reported error as :

2024-04-23 15:51:07,526 INFO Loading regions...
2024-04-23 15:51:08,061 INFO Checking plotting region in matrix...
2024-04-23 15:51:08,072 INFO Loading matrix...
2024-04-23 15:56:47,498 INFO Getting window sizes...
Traceback (most recent call last):
  File "/home/wang_group/.local/bin/tadtool", line 448, in <module>
    TADtool()
  File "/home/wang_group/.local/bin/tadtool", line 44, in __init__
    getattr(self, args.command)()
  File "/home/wang_group/.local/bin/tadtool", line 163, in plot
    window_sizes = np.load(args.window_sizes[0])
  File "/usr/local/lib/python3.6/dist-packages/numpy/lib/npyio.py", line 444, in load
    raise ValueError("Cannot load file containing pickled data "
ValueError: Cannot load file containing pickled data when allow_pickle=False

My window.txt file is as :

LG14 9000000 9020000
LG14 9020000 9040000
LG14 9040000 9060000
LG14 9060000 9080000
LG14 9080000 9100000
LG14 9100000 9120000
LG14 9120000 9140000
LG14 9140000 9160000
LG14 9160000 9180000
LG14 9180000 9200000
...

Is my window.txt file in a wrong format? The default window size calculated by the tool is 100K, which is too large for me, I'd like it to be 20k or more little.