stefanpeidli / mousipy Goto Github PK

Hi all,

After installing mousipy with pip, I ran the recommended code and received this error:

import scvelo as scv
from mousipy import translate

FileNotFoundError: [Errno 2] No such file or directory: 'src/mousipy/biomart/human_to_mouse_biomart_export.csv'

Do I need to download this csv?

Hi!
Are you planning to add a function that can translate from human genes to mouse genes?
Best, Sandra

Could you please help?
import scvelo as scv
from mousipy import translate
humanized_mdata = translate(mdata)

AttributeError Traceback (most recent call last)
Input In [219], in <cell line: 3>()
1 import scvelo as scv
2 from mousipy import translate
----> 3 humanized_mdata = translate(mdata)

File ~/ENTER/lib/python3.9/site-packages/mousipy/mousipy.py:196, in translate(adata, stay_sparse)
193 # for those with an entry but no ortholog we assume that there really is no known ortholog
194 # which means we ignore genes in m2h_no_hit
195 bdata = translate_direct(adata, direct, no_index)
--> 196 bdata = translate_multiple(bdata, adata, multiple, stay_sparse=stay_sparse)
197 bdata = collapse_duplicate_genes(bdata, stay_sparse=stay_sparse)
198 return bdata

File ~/ENTER/lib/python3.9/site-packages/mousipy/mousipy.py:122, in translate_multiple(adata, original_data, multiple, stay_sparse)
106 """Adds the counts of multiple-hit genes to ALL their orthologs.
107 Parameters
108 ----------
(...)
119 Updated original adata.
120 """
121 from scipy.sparse import csr_matrix, hstack
--> 122 X = adata.X.copy() if stay_sparse else adata.X.A.copy()
123 var = adata.var.copy()
124 for mgene, hgenes in tqdm(multiple.items(), leave=False):

AttributeError: 'numpy.ndarray' object has no attribute 'A'