convertFormat(ldat.mod.se, from = "sce", to="loom", outFile = "~/Desktop/ldat.loom")
You created a large dataset with compression and chunking.
The chunk size is equal to the dataset dimensions.
If you want to read subsets of the dataset, you should testsmaller chunk sizes to improve read times.
You created a large dataset with compression and chunking.
The chunk size is equal to the dataset dimensions.
If you want to read subsets of the dataset, you should testsmaller chunk sizes to improve read times.
Error in H5Ldelete(h5loc = loc$H5Identifier, name = name) :
Specified link doesn't exist.
In addition: Warning message:
In .regularise_df(SummarizedExperiment::colData(obj), drop_single_values = drop_single_values) :
Dropping single category variables:orig.ident, ident
Conversion successfully created a loom file however, when I tried to import the file in question to scvelo as follows;
-------------------------------------------------------------------------
KeyError Traceback (most recent call last)
<ipython-input-11-c43bed4d070b> in <module>
----> 1 ldata=scv.read_loom("/Volumes/Documents/R/ldat.loom")
/usr/local/Cellar/python@3.9/3.9.2_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/anndata/_io/read.py in read_loom(filename, sparse, cleanup, X_name, obs_names, obsm_names, var_names, varm_names, dtype, **kwargs)
192 from loompy import connect
193
--> 194 with connect(filename, "r", **kwargs) as lc:
195 if X_name not in lc.layers.keys():
196 X_name = ""
/usr/local/Cellar/python@3.9/3.9.2_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/loompy/loompy.py in connect(filename, mode, validate, spec_version)
1387 Note: if validation is requested, an exception is raised if validation fails.
1388 """
-> 1389 return LoomConnection(filename, mode, validate=validate)
/usr/local/Cellar/python@3.9/3.9.2_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/loompy/loompy.py in __init__(self, filename, mode, validate)
79 if validate:
80 lv = loompy.LoomValidator()
---> 81 if not lv.validate(filename):
82 raise ValueError("\n".join(lv.errors) + f"\n{filename} does not appead to be a valid Loom file according to Loom spec version '{lv.version}'")
83
/usr/local/Cellar/python@3.9/3.9.2_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/loompy/loom_validator.py in validate(self, path, strictness)
49 if self.version == None:
50 self.version = get_loom_spec_version(f)
---> 51 valid1 = self.validate_spec(f)
52 if not valid1:
53 self.errors.append("For help, see http://linnarssonlab.org/loompy/format/")
/usr/local/Cellar/python@3.9/3.9.2_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/loompy/loom_validator.py in validate_spec(self, file)
202 if self.version == "3.0.0":
203 self._check("attrs" in file, "Global attributes missing")
--> 204 for attr in file["attrs"]:
205 if type(attr) is np.ndarray:
206 delay_print(f"{attr: >{width}} {attr.dtype} {attr.shape}")
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
/usr/local/Cellar/python@3.9/3.9.2_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/h5py/_hl/group.py in __getitem__(self, name)
286 raise ValueError("Invalid HDF5 object reference")
287 else:
--> 288 oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
289
290 otype = h5i.get_type(oid)
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/h5o.pyx in h5py.h5o.open()
KeyError: "Unable to open object (object 'attrs' doesn't exist)"
I got a similar error when I tried to import in R
ldat.test<-ReadVelocity("/Volumes/Documents/R/ldat.loom", verbose = T)
reading loom file via hdf5r...
Error in `[[.H5File`(f, "col_attrs/CellID") :
An object with name col_attrs/CellID does not exist in this group
I've been absolute getting stuck in the conversion and I'd really appreciate any help.
Hi ,
I have this sce file;
and converted to loom by a following warmings;
Conversion successfully created a loom file however, when I tried to import the file in question to scvelo as follows;
ldata=scv.read_loom("/Volumes/Documents/R/ldat.loom")
I got a similar error when I tried to import in R
I've been absolute getting stuck in the conversion and I'd really appreciate any help.
THanks.