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yollct / spycone

Spicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data
GNU General Public License v3.0
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Test data error #5

Open Tang-pro opened 6 months ago

Tang-pro commented 6 months ago

Hi， @yollct `subprocess.call("wget https://zenodo.org/record/7228475/files/tutorial_alt_sorted_bc_tpm.csv?download=1 -O alt_sorted_bc_tpm.csv", shell=True) subprocess.call("wget https://zenodo.org/record/7228475/files/tutorial_alt_genelist.csv?download=1 -O alt_genelist.csv", shell=True)

data = pd.read_csv("alt_sorted_bc_tpm.csv", sep="\t") genelist = pd.read_csv("alt_genelist.csv", sep="\t")

geneid= list(map(lambda x: str(int(x)) if not np.isnan(x) else x, genelist['gene'].tolist())) transcriptid = genelist['isoforms'].to_list()

dset = spy.dataset(ts=data, transcript_id=transcriptid, gene_id = geneid, species=9606, timepts=4, reps1=3)`

thr error message is Traceback (most recent call last): File "", line 1, in File "/public/home/zwliu/miniconda3/lib/python3.10/site-packages/spycone/DataSet.py", line 197, in init self._get_gene_level() File "/public/home/zwliu/miniconda3/lib/python3.10/site-packages/spycone/DataSet.py", line 226, in _get_gene_level self.genelevel_symb.append(self.symbs[v[0]]) IndexError: too many indices for array: array is 0-dimensional, but 1 were indexed

What is the reason for this and how to solve it? If it is not a model species, can the species parameter be eliminated?

yollct commented 6 months ago

Hi,

I guess this error is due to the symbs parameter is None, could you please try inputting something there, like with geneid?

Best,

Chit Tong