Error of cell_type_specific_TF_RE_binding_chr() function

[xiaoxiao6630]

Hello,

I used LINGER 1.67 version. I had errors showing "raise KeyError(f"{not_found} not in index")" when I run LL_net.cell_type_specific_TF_RE_binding(GRNdir,adata_RNA,adata_ATAC,genome,celltype,outdir,method) using example data and pipeline.

Then I checked the source code and tested code by line, I think there are errors of function **cell_type_specific_TF_RE_binding_chr()**.

1. First error is RE=RE.loc[N_overlap], I changed it into set_N_overlap = set(N_overlap) overlap_index = RE.index.isin(set_N_overlap) RE = RE[overlap_index]; but then I have new error of S = np.log(RE_cluster+0.1) + np.log(mat+TFbinding+0.1) + np.log(TF_cluster+0.1).

Could you help to check this function?

Thanks!

[xiaoxiao6630]

I found how to fix this problem, I changed the lines RE=pd.DataFrame(adata_ATAC.X.T,index=adata_ATAC.var['gene_ids'].values,columns=adata_ATAC.obs['barcode'].values) into RE=pd.DataFrame(adata_ATAC.raw.X.toarray().T,index=adata_ATAC.raw.var['gene_ids'].values,columns=adata_ATAC.obs['barcode'].values). Then it works.

Thanks!

[yojetsharma]

Were you able the run the whole tutorial? Because several others have pointed out that they're facing the following error:

import LingerGRN.LL_net as LL_net
LL_net.cell_type_specific_TF_RE_binding(GRNdir,adata_RNA,adata_ATAC,genome,celltype,outdir,method)
Generate cell type specitic TF binding potential for cell type Radial-glia-3...

  0%|                                                                                                                                                                                                                           | 0/22 [00:00<?, ?it/s]

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[14], line 2
      1 import LingerGRN.LL_net as LL_net
----> 2 LL_net.cell_type_specific_TF_RE_binding(GRNdir,adata_RNA,adata_ATAC,genome,celltype,outdir,method)

File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/LingerGRN/LL_net.py:501, in cell_type_specific_TF_RE_binding(GRNdir, adata_RNA, adata_ATAC, genome, celltype, outdir, method)
    499     for i in tqdm(range(22)):
    500         chrN='chr'+str(i+1)
--> 501         mat=pd.read_csv(outdir+chrN+'_cell_population_TF_RE_binding.txt',sep='\t',index_col=0,header=0)
    502         out=cell_type_specific_TF_RE_binding_chr(adata_RNA,adata_ATAC,GRNdir,chrN,genome,label0,outdir,method,mat)
    503 #result=pd.concat([result,out],axis=1).fillna(0)

File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/pandas/io/parsers/readers.py:912, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, date_format, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options, dtype_backend)
    899 kwds_defaults = _refine_defaults_read(
    900     dialect,
    901     delimiter,
   (...)
    908     dtype_backend=dtype_backend,
    909 )
    910 kwds.update(kwds_defaults)
--> 912 return _read(filepath_or_buffer, kwds)

File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/pandas/io/parsers/readers.py:577, in _read(filepath_or_buffer, kwds)
    574 _validate_names(kwds.get("names", None))
    576 # Create the parser.
--> 577 parser = TextFileReader(filepath_or_buffer, **kwds)
    579 if chunksize or iterator:
    580     return parser

File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/pandas/io/parsers/readers.py:1407, in TextFileReader.__init__(self, f, engine, **kwds)
   1404     self.options["has_index_names"] = kwds["has_index_names"]
   1406 self.handles: IOHandles | None = None
-> 1407 self._engine = self._make_engine(f, self.engine)

File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/pandas/io/parsers/readers.py:1661, in TextFileReader._make_engine(self, f, engine)
   1659     if "b" not in mode:
   1660         mode += "b"
-> 1661 self.handles = get_handle(
   1662     f,
   1663     mode,
   1664     encoding=self.options.get("encoding", None),
   1665     compression=self.options.get("compression", None),
   1666     memory_map=self.options.get("memory_map", False),
   1667     is_text=is_text,
   1668     errors=self.options.get("encoding_errors", "strict"),
   1669     storage_options=self.options.get("storage_options", None),
   1670 )
   1671 assert self.handles is not None
   1672 f = self.handles.handle

File ~/miniconda3/envs/LINGER/lib/python3.10/site-packages/pandas/io/common.py:859, in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)
    854 elif isinstance(handle, str):
    855     # Check whether the filename is to be opened in binary mode.
    856     # Binary mode does not support 'encoding' and 'newline'.
    857     if ioargs.encoding and "b" not in ioargs.mode:
    858         # Encoding
--> 859         handle = open(
    860             handle,
    861             ioargs.mode,
    862             encoding=ioargs.encoding,
    863             errors=errors,
    864             newline="",
    865         )
    866     else:
    867         # Binary mode
    868         handle = open(handle, ioargs.mode)

FileNotFoundError: [Errno 2] No such file or directory: '/home/user/Desktop/linger/chr1_cell_population_TF_RE_binding.txt'