Error in diopy.input.read_rds

[ElyasMo]

Hi and thanks for developing such a helpful toolkit

I was trying to read in a scRNA-seq.rds file python using the bellow mentioned code and this error pop up :
It seems that it is reading the .rds file as _tmp.h5

Any help would be appreciated

scRNA_seq = diopy.input.read_rds(file="./scRNAseq.rds",assay_name="RNA",object_type="seurat")



sh: 1: Rscript: not found
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[74], line 1
----> 1 scRNA_seq = diopy.input.read_rds(file="./scRNAseq.rds",assay_name="RNA",object_type="seurat")

File ~/.local/lib/python3.10/site-packages/diopy/input.py:604, in read_rds(file, object_type, assay_name)
    602 os.system('Rscript ' + diopyr_file +' -r '+ file + ' -t ' + object_type + ' -a ' + assay_name)
    603 tmp = re.sub('.rds', '_tmp.h5', file)
--> 604 adata = read_h5(file =tmp, assay_name = assay_name)
    605 return adata

File ~/.local/lib/python3.10/site-packages/diopy/input.py:51, in read_h5(file, assay_name)
     49 if file is None:
     50     raise OSError('No such file or directory')
---> 51 h5 = h5py.File(name=file, mode='r')
     52 try:
     53     adata = h5_to_adata(h5=h5, assay_name=assay_name)

File /usr/local/lib/python3.10/dist-packages/h5py/_hl/files.py:567, in File.__init__(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, fs_page_size, page_buf_size, min_meta_keep, min_raw_keep, locking, alignment_threshold, alignment_interval, meta_block_size, **kwds)
    558     fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0,
    559                      locking, page_buf_size, min_meta_keep, min_raw_keep,
    560                      alignment_threshold=alignment_threshold,
    561                      alignment_interval=alignment_interval,
    562                      meta_block_size=meta_block_size,
    563                      **kwds)
    564     fcpl = make_fcpl(track_order=track_order, fs_strategy=fs_strategy,
    565                      fs_persist=fs_persist, fs_threshold=fs_threshold,
    566                      fs_page_size=fs_page_size)
--> 567     fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
    569 if isinstance(libver, tuple):
    570     self._libver = libver

File /usr/local/lib/python3.10/dist-packages/h5py/_hl/files.py:231, in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
    229     if swmr and swmr_support:
    230         flags |= h5f.ACC_SWMR_READ
--> 231     fid = h5f.open(name, flags, fapl=fapl)
    232 elif mode == 'r+':
    233     fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File h5py/h5f.pyx:106, in h5py.h5f.open()

FileNotFoundError: [Errno 2] Unable to open file (unable to open file: name = './scRNAseq_tmp.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)