Open BioTechTimy opened 2 years ago
To recreate using https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3674239,
import stream from scipy.io import mmread import pandas as pd name = 'GSM3674239_b1' x = mmread('data/' + name + '.matrix.mtx') gene_names = pd.read_csv('data/' + name + '.genes.tsv', sep = '\t', header=None) barcodes = pd.read_csv('data/' + name + '.barcodes.tsv', sep = '\t', header=None) df = pd.DataFrame.sparse.from_spmatrix(x, index = gene_names.iloc[:, 1], columns = name + '-bone-' + barcodes.iloc[:, 0]) df.to_pickle("df.pkl") df_stream = stream.read('df.pkl')
Traceback
--------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-12-24a97f60ba4b> in <module> ----> 1 df_stream = stream.read('merged_df.pkl') 2 #stream.cal_qc(df_stream,assay='rna') 3 #stream.plot_qc(df_stream,jitter=0.3) ~/miniconda/envs/venv_stream/lib/python3.7/site-packages/stream/core.py in read(file_name, file_path, file_format, delimiter, workdir, file_sample, file_feature, **kwargs) 185 f.close() 186 --> 187 if('workdir' not in adata.uns_keys()): 188 set_workdir(adata,workdir=workdir) 189 else: ~/miniconda/envs/venv_stream/lib/python3.7/site-packages/pandas/core/generic.py in __getattr__(self, name) 5476 ): 5477 return self[name] -> 5478 return object.__getattribute__(self, name) 5479 5480 def __setattr__(self, name: str, value) -> None: AttributeError: 'DataFrame' object has no attribute 'uns_keys'
Thank you Timothy Daley
Any update on this? It seems like stream can't read in standard pandas data frames. Is there documentation that I can read for what the expected input should be?
To recreate using https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3674239,
Traceback
Thank you Timothy Daley