Test data error

[Tang-pro]

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]

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

[alexandregayCRCT]

Hello @yollct ,
The tip works.
Would it be possible to update readthedocs with this information, as well as the removal of the keygen parameter?
dset = spy.dataset(ts=data,
transcript_id=transcriptid,
gene_id = geneid,
species=9606,
timepts=4,
reps1=3,
symbs=geneid)

Best,
Alex