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liu-bioinfo-lab / caesar

An accurate and interpretable computational model for predicting nucleosome resolution chromatin contact maps
MIT License
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When I run the code, there are some problems when loading epigenomic data (CTCF) and store into arrays #3

Open HappyLife-together opened 1 year ago

HappyLife-together commented 1 year ago

run 01_generate_example_input_regions.py

Step 2: Load epigenomic data and store into arrays DNase_seq CTCF Traceback (most recent call last): File "01_generate_example_input_regions.py", line 221, in epigenomic2array(bigwig_path, epi_names, [i for i in ch_coord.keys()], epi_folder) File "01_generate_example_input_regions.py", line 157, in epigenomic2array load_bigWig_for_entire_genome(f'{input_path}.bigWig', epi_name, chroms, epi_path=ouput_folder) File "01_generate_example_input_regions.py", line 112, in load_bigWig_for_entire_genome vec = bw.stats(ch, 0, end_pos, exact=True, nBins=nBins) RuntimeError: Invalid interval bounds!

dmcbffeng commented 1 year ago

Thank you for the feedback! Actually, we used bedGraph in our runs. When uploading the data for sharing, we used the original bigWig data to minimize the storage space. But it seems pyBigWig will raise some issues when the boundary exceeds the chrom size.

Now we re-upload the bedGraph files and removed the bigWig files. You could download them from the same DropBox link and it should work this time.