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LoomR and ScopeLoomR can read these two files, but Loompy reports that it cannot read them. #171

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sunjiahe-hub opened this issue Apr 25, 2022 · 0 comments

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@sunjiahe-hub
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sunjiahe-hub commented Apr 25, 2022

Hi, in the process of my analysis. I found that these two files cannot be read by Loompy, and the following error will be reported. I tried to use LoomR and ScopeLoomR to read the files, and found that they can be read. I hope to get your help, thank you.
file download address:
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE176nnn/GSE176173/suppl/GSE176173_Talon_Naive_TSC_PRC2_loom.loom.gz
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE176nnn/GSE176173/suppl/GSE176173_Talon_Naive_TSC_PRC2_loom.loom.gz

`E:\anaconda3\python.exe D:/sgs-project/LoomParser/LoomParser.py
Traceback (most recent call last):
File "D:/sgs-project/LoomParser/LoomParser.py", line 58, in
LoomParser(in_file_path, out_file_path)
File "D:/sgs-project/LoomParser/LoomParser.py", line 24, in LoomParser
ds = loompy.connect(in_file_path)
File "E:\anaconda3\lib\site-packages\loompy\loompy.py", line 1515, in connect
return LoomConnection(filename, mode, validate=validate)
File "E:\anaconda3\lib\site-packages\loompy\loompy.py", line 86, in init
raise ValueError("\n".join(lv.errors) + f"\n{filename} does not appear to be a valid Loom file according to Loom spec version '{lv.version}'")
ValueError: Row attribute 'Gene' dtype object is not allowed
Column attribute 'CellID' dtype object is not allowed
Column attribute 'Embedding' dtype [('_X', '<f8'), ('_Y', '<f8')] is not allowed
Column attribute 'Embeddings_X' dtype [('-1', '<f8')] is not allowed
Column attribute 'Embeddings_Y' dtype [('-1', '<f8')] is not allowed
Column attribute 'annotation' dtype object is not allowed
Column attribute 'cluster' dtype object is not allowed
For help, see http://linnarssonlab.org/loompy/format/
./data/5_GSE176173_Talon_Naive_TSC_PRC2_loom.loom does not appear to be a valid Loom file according to Loom spec version '0.0.0'

Process finished with exit code 1`

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