Thanks a lot for supporting Python3 and the cool file, it very useful for me.
But when I use this new version to process my own data, I found there are some problem. The error message like this:
tadlib.hitad.genomeLev DEBUG @ 12/01/18 13:49:56: Chrom Y:
tadlib.hitad.genomeLev DEBUG @ 12/01/18 13:49:56: resolution: 5000, rep1
tadlib.hitad.genomeLev DEBUG @ 12/01/18 13:49:56: Cache Chrom object into /home/nanguage/.hitad/tmpq1ukaxsj20181201134956 ...
tadlib.hitad.genomeLev DEBUG @ 12/01/18 13:49:59: Chrom MT:
tadlib.hitad.genomeLev DEBUG @ 12/01/18 13:49:59: resolution: 5000, rep1
Traceback (most recent call last):
File "/home/nanguage/S/miniconda3/bin/hitad", line 107, in run
G = Genome(args.datasets, args.maxsize, cachefolder)
File "/home/nanguage/S/miniconda3/lib/python3.6/site-packages/tadlib/hitad/genomeLev.py", line 89, in __init__
work = Chrom(chrom, res, tdata, rep, maxsize)
File "/home/nanguage/S/miniconda3/lib/python3.6/site-packages/tadlib/hitad/chromLev.py", line 105, in __init__
IF[np.isnan(IF)] = 0
TypeError: ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''
Then I try to debug it, I found that this error occurs when there are small or empty matrix in the cool file (like the 'chrMT' in above case, it's a very small matrix). I know, I can prevent this by rebuild the cool file exclude the 'chrMT', but I think this is an undefined behavior, program should ignore it instead of interrupted. So I fix this by modify a few lines of code, maybe it is not a good solution, but it works for this situtation.
Hello,
Thanks a lot for supporting Python3 and the cool file, it very useful for me. But when I use this new version to process my own data, I found there are some problem. The error message like this:
Then I try to debug it, I found that this error occurs when there are small or empty matrix in the cool file (like the 'chrMT' in above case, it's a very small matrix). I know, I can prevent this by rebuild the cool file exclude the 'chrMT', but I think this is an undefined behavior, program should ignore it instead of interrupted. So I fix this by modify a few lines of code, maybe it is not a good solution, but it works for this situtation.