copy number signature

[hfl112]

Hi , I am trying to get the CN signature based on copy number 48 matrix. I don't know whether I missed something:

• I've generate the CN matrix by CNVMatrixGenerator.py:

  
  MutationType | TCGA-OR-A5J4-01 | TCGA-OR-A5J5-01 | TCGA-OR-A5J6-01 | TCGA-OR-A5J7-01 | TCGA-OR-A5J9-01 | TCGA-OR-A5JC-01
  -- | -- | -- | -- | -- | -- | --
  0:homdel:0-100kb | 1 | 1 | 0 | 1 | 0 | 0
  0:homdel:100kb-1Mb | 1 | 1 | 0 | 0 | 1 | 1
  0:homdel:>1Mb | 0 | 0 | 0 | 0 | 0 | 0
  1:LOH:0-100kb | 12 | 1 | 4 | 6 | 2 | 6
  1:LOH:100kb-1Mb | 35 | 0 | 0 | 9 | 9 | 5
  1:LOH:1Mb-10Mb | 14 | 0 | 0 | 11 | 14 | 2
  1:LOH:10Mb-40Mb | 4 | 0 | 0 | 5 | 2 | 3
  1:LOH:>40Mb | 0 | 0 | 0 | 0 | 1 | 1

- I want to calculate the CN signature contribution for each signature, like : https://cancer.sanger.ac.uk/signatures/cn/.Then I ran spss:

########################################################## Exacting Profile for Sample 1

TypeError Traceback (most recent call last) Cell In[17], line 5 2 input_f = "/home/UTHSCSA/hef/2.Project/6.WGD/2.analysis/8.signature/CN_sig/CN_WGD.CNV48.matrix.tsv" 3 data = pd.read_table(input_f) ----> 5 spss.single_sample(data, wdir + "/results", ref="GRCh38.p12", exome=False)

File ~/Tools/miniconda3/lib/python3.8/site-packages/sigproSS/signatures_optimizer.py:239, in add_signatures(W, genome, cutoff, presentSignatures, toBeAdded) 237 #print(len(notToBeAdded)) 238 originalSimilarity = -1 # it can be also written as oldsimilarity --> 239 maxmutation = round(np.sum(genome)) 240 init_listed_idx = presentSignatures 241 init_nonlisted_idx = list(set(list(range(W.shape[1])))-set(init_listed_idx)-set(notToBeAdded))

TypeError: type str doesn't define round method

I changed round() to np.round() in "signatures_optimizer.py",  got other errors:

File ~/Tools/miniconda3/lib/python3.8/site-packages/numpy/core/fromnumeric.py:43, in _wrapit(obj, method, *args, *kwds) 41 except AttributeError: 42 wrap = None ---> 43 result = getattr(asarray(obj), method)(args, **kwds) 44 if wrap: 45 if not isinstance(result, mu.ndarray):

TypeError: ufunc 'rint' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

Thanks in advance

[hfl112]

Found an issue posted here: https://github.com/AlexandrovLab/SigProfilerExtractor/issues/136 It works for me.